System for three-way combinatorial crispr screens for analysing target interactions and methods thereof

ABSTRACT

Provided is a system for multiplexed genome editing or a two or three-way combinatorial CRISPR screening. Also provided is high-throughput screening of disease-alleviating genetic combinations to identify two-way and three-way synergistic drug combinations as potential treatment regimens. Also provided is a lentiviral three-way combinatorial guide RNA expression cassette and combinatorial guide RNA libraries.

This international patent application claims the benefit of U.S. Provisional Patent Application No.: 63/010,877 filed on Apr. 16, 2020, the entire content of which is incorporated by reference for all purpose.

1. FIELD

Provided herein is a system for multiplexed genome editing or a two or three-way combinatorial CRISPR screening. Also provided is high-throughput screening of disease-alleviating genetic combinations to identify two-way and three-way synergistic drug combinations as potential treatment regimens. Also provided is a lentiviral three-way combinatorial guide RNA expression cassette and combinatorial guide RNA libraries.

2. BACKGROUND

Despite the promise of combination therapies to enhance treatment efficacy for various diseases (Al-Lazikani et al., 2012), only a limited number of effective combinations, especially those comprising three or more drugs (Table S1), have been discovered so far. Drug combination effect is difficult to predict due to unanticipated synergy or antagonism, and is not simply the sum of the effects brought by each drug (Borisy et al., 2003). Microplate arrays are coupled to robotics systems to screen large panels of drug combinations. However, as the number of experiments grows exponentially with the number of drugs and the order of combinatorial complexity being studied, such approach can become prohibitively expensive. RNA interference and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based genetic perturbation systems have been applied to facilitate the screening of effective drug target pairs (Doench, 2018; Wong et al., 2016b), but no library assembly and screening method has been validated to simultaneously evaluate more than two targets. This could be attributed to the relatively low and variable cleavage efficiency for polycistronic systems to express multiple RNAs (Han et al., 2017; Xu et al., 2017), and/or the characterization of high-order combinations requires large-scale oligo synthesis and high sequencing costs (elaborated in Design). Mathematical models have been developed for predicting three-way and higher-order drug interactions (Cokol et al., 2017; Wood et al., 2012; Zimmer et al., 2016), but high-throughput methods are needed to experimentally validate sets of potential combinations. Breaking through the bottlenecks, here we establish and validate an extensible platform (named CombiGEM-CRISPR v2.0) for rapid screening of disease-alleviating gene knockouts to study high-order genetic interactions, identify potential therapeutic target combinations, and deploy their matching drug regimens for further testing.

3. SUMMARY

Provided is a CRISPR-based multi-gene knockout screening system and new toolkits for extensible assembly of barcoded high-order combinatorial guide RNA libraries en masse. We apply this system for systematically identifying not only pairwise but also three-way synergistic therapeutic target combinations, and successfully validated double and triple combination regimens for suppression on cancer cell growth and protection against Parkinson's disease-associated toxicity. This system overcomes the practical challenges to experiment on a large number of high-order genetic and drug combinations and is applicable for uncovering the rare synergistic interactions between druggable targets.

Systematically characterizing genetic interactions among multiple (i.e. more than two) elements. One application of this system is to enable high-throughput screening of disease alleviating genetic combinations to identify two-way and even three-way synergistic drug combinations as potential treatment regimens. Drug combination effect is difficult to predict due to unanticipated synergy or antagonism and is not simply the sum of the effects brought by each drug. Discovering effective drug combinations for diseases has been a major challenge because of the technical difficulties in systematically screening a vast number of possible combinations. For example, microplate arrays are coupled to robotics systems to screen large panels of drug combinations. However, as the number of experiments grows exponentially with the number of drugs and the order of combinatorial complexity being studied, such approach requiring a large amount of drugs can become prohibitively expensive. Thus, despite the promise of combination therapies to enhance treatment efficacy for various diseases, only a limited number of effective combinations, especially those comprising more than two drugs, have been discovered so far.

Provided herein is a system for multiplexed genome editing or a two or three-way combinatorial CRISPR screening comprising: a lentiviral vector comprising human U6 (hU6) promoter, mouse U6 (mU6) promoter and human H1 (hH1) promoter expressing an array of three or more barcoded guide RNAs (“gRNAs”) oligo pairs, the promoters having a 3′ end comprising modified hU6, mU6 and hH1 promoter sequences for paired annealing of the barcoded gRNAs oligo pairs.

Provided herein is a system for multiplexed genome editing or a two or three-way combinatorial CRISPR screening comprising: a lentiviral vector comprising human U6 (hU6) promoter, mouse U6 (mU6) promoter and human H1 (hH1) promoter expressing an array of three or more barcoded guide RNAs (“gRNAs”) oligo pairs, the hU6 promoter having an unmodified promoter sequence at 3′ end and the mU6 and hH1 promoters having modified promoter sequences at 3′ end for paired annealing of the barcoded gRNAs oligo pairs.

In one embodiment, the paired annealing of the barcoded gRNAs oligo pairs form RNA scaffolds.

In one embodiment, the combinatorial gRNA library is assembled by CombiGEM-CRISPR v2.0.

In one embodiment, the lentiviral vector transfects human cells and the barcoded gRNAs are delivered to the human cells.

In one embodiment, the system further comprising quantitation of barcoded gRNAs using next-generation sequencing at a time point post transfection.

In one embodiment, the three-way combinatorial CRISPR screen is a high-throughput screen.

In one embodiment, the gRNAs form a RNA scaffold sequence comprising the same 3′ end of the modified hU6, mU6 and hH1 promoter sequences as the combinatorial gRNA libraries.

In one embodiment, the gRNAs form a RNA scaffold sequence comprising the same 3′ end of the hU6, mU6 and hH1 promoter sequences as the combinatorial gRNA libraries.

Provided herein is a method to screen for at least a three-way drug target combination; said method comprises: (i) providing a gRNA library targeting druggable genes of HGSOC wherein each gene comprises an array of 3 gRNAs; (ii) transfecting human cells; and (iii) quantifying barcoded gRNAs using next-generation sequencing.

Provided herein is a system to screen for at least a three-way drug target combination comprising: (i) providing a lentiviral three-way combinatorial gRNA expressing construct that express gRNAs; (ii) transfecting human cells with fluorescence reporter gene; and (iii) measuring percentage of cell population positive for fluorescence at a time period post-transfection.

In one embodiment, the fluorescence is measured using a flow cytometry and wherein the fluorescence is GFP, RFP and BFP fluorescence.

In one embodiment, the gRNAs target an exonic regions of green (GFP), red (RFP), and blue (BFP) fluorescent protein reporter genes.

In one embodiment, the human cells are ovarian cancer cells.

In one embodiment, the ovarian cancer cells are high-grade serous ovarian cancer (“HGSOC”) cells.

In one embodiment, the ovarian cancer cells are OVCAR8-ADR and OVCAR8-ADR-Cas9.

Provided herein is a method to screen for at least a three-way drug target combination comprising the steps of: (i) providing a lentiviral three-way combinatorial gRNA expressing construct that express gRNAs; (ii) transfecting human cells with fluorescence reporter gene; and (iii) measuring percentage of cell population positive for fluorescence at a time period post-transfection.

In one embodiment, the method further comprising validation of the three-way drug target combination by matching a drug to the drug target.

In one embodiment, the three-way drug target combinations provides a three-drug regimen for a disease.

In one embodiment, the fluorescence is GFP, RFP or BFP.

In one embodiment, the at least a three-way drug target combination are synergistic combinations.

In one embodiment, the disease is cancer or Parkinson's disease.

Provided herein is a method to treat HGSOC comprising administering drugs that targets PARP1, DNMT1, CDK2, FKBP1A or a combination thereof.

In one embodiment, the drug comprises Olaparib (OLA), azacitdine (AZA), seliciclib (SEL), sirolimus (SIR), or a combination thereof.

In one embodiment, the drug comprises OLA and AZA.

Provided herein is a system for CRISPR-based multi-gene knockout screening comprising a barcoded gRNA expression cassette comprising: (i) a first promoter operatively linked to a first gRNA; (ii) a second promoter operatively linked to a second gRNA; (iii) a third promoter operatively linked to a third gRNA; and (iv) three barcoded gRNA sequencing region, wherein the gRNA expression cassette is in a single vector.

In one embodiment, the promoters are human U6, mouse U6, and Human H1 promoters and the three barcoded gRNA are modified gRNA scaffold variants.

In one embodiment, the promoters comprises a modified 3′ end sequence which are complementary to the modified gRNA scaffold variants, said 3′ end sequence anneals to the modified gRNA scaffold variants.

In one embodiment, the system further comprising: (i) pooled digestion and ligation of the annealed 3′ end sequence and the gRNA scaffold variants to form an assembly of pooled barcoded combinatorial gRNA library.

In one embodiment, the expression cassettes knockout target GFP gene in OVACR8-ADR-Cas9 cells.

In one embodiment, the gRNA scaffold variants comprises: (i) higher on-target activity than wild-type scaffold; (ii) low off-target activities; and (iii) high on-to-off target activity.

Provided herein is a system for CRISPR-based multi-gene knockout screening comprising a barcoded gRNA expression cassette comprising v3.11, v.3.12 or v.3.13.

4. BRIEF SUMMARY OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 . Evaluation of the extensibility of existing methods and possible toolkits for assembling three-way gRNA combinations for screening.

FIG. 2 . Overview of CombiGEM-CRISPR v2.0

The workflow starts with the synthesis of barcoded gRNA oligo pairs, which are annealed and cloned into gRNA expression vectors in pooled format. Only one set of oligos is needed for building the libraries of higher-order gRNA combinations for multiplexed CRISPR screens, as the 3′ end of promoters are sequence-adapted to the sticky ends of the annealed oligos. Barcoded combinatorial gRNA library is assembled multiplicatively using one-pot reactions as described in FIG. 6 , and delivered into human cells by lentiviruses. Barcoded representations within cell pools are quantified using next-generation sequencing. Then, validation is done by using matching drugs. Pre-assembled libraries can also be flexibly extended to higher-order ones, or a more focused library can be constructed using a subset of the same oligos, for a secondary screen.

FIG. 3 . Functional disruption of multiple genes using a CRISPR-Cas9-based multi-gene knockout system

Lentiviral delivery of combinatorial gRNA expression constructs efficiently disrupt multiple target genes. Flow cytometry was used to measure the percentage of cell populations positive for GFP, RFP, and BFP fluorescence at day 11-14 post-infection in OVCAR8-ADR and OVCAR8-ADR-Cas9 cells. Data are mean±SD, n=3 biological replicates.

FIG. 4 . A CRISPR-based triple-gene knockout screen identifies synergistic three-way combinations that inhibit ovarian cancer cell growth

(A) Distributions of barcode reads in the plasmid and infected OVCAR8-ADR-Cas9 cell pools. A high-coverage three-way combinatorial gRNA library (99.8% of all expected gRNA combinations; 32,705 out of 32,768) was obtained in both the plasmid and cell pools. Most barcoded gRNA combinations were detected within a 5-fold range from the mean barcode reads per combination (highlighted by the shaded areas).

(B) High correlation between barcode representations (normalized barcode counts) within the plasmid pool and infected cell pool indicates efficient lentiviral delivery of the three-way combinatorial gRNA library into cells. The horizontal dotted lines in the Bland-Altman plots indicate the 95% limits of agreement.

(C-D) High reproducibility for barcode representations between two biological replicates in cells cultured for 15-day (C), and 26-day (D) post-infection with the three-way combinatorial gRNA library. The horizontal dotted lines in the Bland-Altman plots indicate the 95% limits of agreement. The vertical dash line indicates the threshold of 100 raw barcode counts.

(E) The coefficient of variation (CV; defined as SD/mean of the fold changes of normalized barcode counts for 26-day versus 15-day cultured cells) was determined for the two biological replicates. Over 94.8% of pairwise gRNA combinations had a CV of <1 in the screen.

(F) OVCAR8-ADR-Cas9 cells infected with the barcoded three-way combinatorial gRNA library were cultured for 15 and 26 days. Barcode representations within the cell pools were quantified using Illumina HiSeq. The barcoded library vector uses hH1-gRNA-WT scaffold, hU6-gRNA-v1 scaffold, and mU6-gRNA-v2 scaffold in the first, second, and third expression cassettes, respectively.

(G) A plot of screen data showing the abundance changes of each barcoded gRNA combinations at day 26 versus day 15 post-infection (in mean log₂ (Fold Change); x-axis) and their genetic interaction (GI₃) score (y-axis). Hit combinations, DNMT1+POLA1+EGFR, DNMT1+POLA1+ERBB2, and CDK4+MAP2K1+POLA1, are highlighted in red. Data were collected from two biological replicates.

(H) Comparisons of the mean log₂ (Fold Change) of three-way gRNA hit combinations with their constituent single and pairwise gRNA combinations (see STAR Methods for details). Statistical significance was analysed by one-way ANOVA with Dunnett's post hoc test. * indicates P<0.05.

(I) Viability, determined by MTT assay, of OVCAR8-ADR-Cas9 cells infected with the indicated triple-gene knockouts and controls. Data shown are mean±SD from biological replicates (n=4). Statistical significance was analysed by one-way ANOVA with Tukey's post hoc test. * indicates P<0.05; #P<0.05 indicates the comparisons with the safe harbour loci triple knockouts.

FIG. 5 . Validation of screen hits with matching three-drug regimens

(A) Viability, determined by MTT assay, of OVCAR8-ADR cells treated with AZA-, FLU- and/or ERL. Data shown are mean±SD from biological replicates (n=3). Statistical significance was analysed by one-way ANOVA with Dunnett's post hoc test, * indicates P<0.05.

(B) Colony formation assay of AZA-, FLU- and/or ERL-treated OVCAR8-ADR cells. The colony numbers and areas were quantified. Data shown are mean±SD from biological replicates (n=3). Statistical significance was analysed by one-way ANOVA with Dunnett's post hoc test, * indicates P<0.05.

(C) Surface plots depict the drug synergy of AZA+FLU+ERL (orange) and AZA+FLU+LAP (cyan). Circles on the transparent triangular plane indicate the expected IC₅₀ for each two-drug combination, and the expected IC₅₀ for triple-drug treatment is located at the center of this triangle. Gray dots are the observed IC₅₀s for single- and double-drug treatments. Red dots are the observed IC₅₀s for the triple-drug treatments. Concave or convex colored planes indicate synergistic or antagonistic drug interaction, respectively. FIC₃ is the fractional inhibitory concentration. Views from two angles are displayed (left and right panels).

(D) Viability, determined by MTT assay (left panels), of OVCAR8-ADR cells treated with RIB-, TRA- and/or FLU. Data shown are mean±SD from biological replicates (n=3). Statistical significance was analysed by one-way ANOVA with Dunnett's post hoc test, * indicates P<0.05. Surface plots (right panels) depict the drug synergy of RIB+TRA+FLU, as presented in (C).

FIG. 6 . Strategy for assembling the barcoded gRNA library pools

(A) gRNA expression cassettes with different promoters and scaffold variants generate efficient knockout of the target GFP gene in OVCAR8-ADR-Cas9 cells. GFPsg1 was used. Flow cytometry was performed to measure the percentage of cell populations positive for GFP fluorescence. Data are mean±SD, n=3 biological replicates. Statistical significance was analysed by one-way ANOVA with Tukey's post hoc test. Modifications in the gRNA scaffolds v1 and v2 are shown.

(B) Library assembly procedures. Oligo pairs (Oligo-F and Oligo-R, respectively) were synthesized and annealed to create double-stranded inserts with 20 bp gRNA target sequences, two BbsI sites, 8 bp barcodes, and 5′ overhangs at their ends. The inserts were mixed in equal molar ratio and cloned into three BbsI- and Mfe-digested storage vectors, which contain the hH1, hU6, or mU6 promoters, with one-pot ligation reactions via their compatible ends to create the pooled storage vector libraries. The 3′ end of the promoter sequences of hH1 and mU6 were modified such that the same pool of gRNA oligos can be used for building the libraries. Subsequent single-pot ligation reactions were performed with the BbsI-digested pooled storage vector libraries and an insert containing the gRNA scaffold sequence (WT, v1, or v2), BamHI and EcoRI sites, and 5′ overhangs at their ends to assemble the barcoded gRNA library pools.

FIG. 7 . Activity of gRNAs at targeted genes in OVCAR8-ADR-Cas9 cells

(A) The efficiency of each gRNA was plotted against its on-target efficacy score predicted by Azimuth 2.0. Efficiency of gRNAs targeting the fluorescent reporter genes were determined using flow cytometry, and data for endogenous genes were obtained from our published data (Wong et al., 2016a).

(B-C) Sequencing of targeted allele for cells infected with gRNA expression construct. OVCAR8-ADR-Cas9 cells were infected with lentiviruses encoding the indicated pairwise (B) and three-way combinatorial (C) gRNA expression constructs. The targeted alleles were amplified from the genomic DNA by PCR and cloned into storage vector for Sanger sequencing. The editing efficiency at each targeted locus and the number of individual clones being sequenced are shown.

FIG. 8 . Prediction of on-target and frameshift scores for gRNAs used in the screening libraries

The gRNAs selected for the three-way combinatorial CRISPR screen showed a higher average on-target score and a higher average frameshift scores predicted by inDelphi and FORECasT than those used in the pairwise CRISPR screen. The combined effect brought by both the on-target and frameshift predictions was also evaluated.

FIG. 9 . Growth inhibition induced by simultaneous targeting DNMT1+POLA1+EGFR/ERBB2 and CDK4+MAP2K1+POLA1 genes, but not safe harbour loci

(A-B) OVCAR8-ADR-Cas9 cells were infected with triple-gRNA combinations that target the indicated genes (A), and the respective single and/or double-gRNA combinations (B). The three safe harbour loci being targeted were PPPIRJ2C, THUMPD3-AS1, and CCR5. The gRNAs used in each combination are listed in Table S5. Cell viability was determined by MTT assay. Data are mean±SD from biological replicates (n=4).

FIG. 10 . RNA-Seq analysis of OVCAR8-ADR cells treated with drug combinations

(A) Heatmaps showing the log₂ fold changes of the expression of 3,834 genes that were identified with an FDR<0.05 as differentially expressed in OVCAR8-ADR cells treated with the three-drug regimen (AZA+FLU+ERL), when compared to the untreated control. The log₂ fold changes of the expression of those genes after treating the cells with the corresponding drug pairs are included. Hierarchical clustering of genes and samples was performed based on the Pearson's correlation.

(B) Matrix showing the mapped pathways for the differentially expressed genes, which were at least 20% up-(orange) or down-(blue) regulated in OVCAR8-ADR cells treated with the three-drug regimen (AZA+FLU+ERL) when compared to the untreated control and also had a fold change of >10%, >5%, or <5% in cells treated with the three-drug regimen over all of those treated with the corresponding two-drug regimens. The bar on top of the x-axis indicates the level of fold change detected by different shades of green. Each darken spot indicates that a gene exists in a particular pathway.

FIG. 11 . Synergistic Drug Interactions of AZA-FLU-ERL/LAP in OVCAR-ADR cells assessed at different inhibitory concentrations

Surface plots depicting the drug interactions of AZA+FLU+ERL (orange) and AZA+FLU+LAP (cyan) and the fractional inhibitory concentration (FIC₃) scores are shown. Panel of IC₅₀ is shown in FIG. 5C.

FIG. 12 . Synergistic drug interactions of AZA-FLU-ERL/LAP in OVSAHO cells assessed at different inhibitory concentrations

Surface plots depicting the drug interactions of AZA+FLU+ERL (orange) and AZA+FLU+LAP (cyan) and the fractional inhibitory concentration (FIC₃) scores are shown.

FIG. 13 . A CRISPR-based dual-gene knockout screen identifies drug pairs that inhibit ovarian cancer cell growth

(A) Distributions of barcode reads in the plasmid and 9-day post-infected OVCAR8-ADR-Cas9 cell pools. 99.7% (25,201 out of 25,281) and 99.0% (25,027 out of 25,281) of all expected gRNA combinations was obtained in the plasmid and cell pools, respectively. Most barcoded gRNA combinations were detected within a 5-fold range from the mean barcode reads per combination (highlighted by the shaded areas).

(B) High correlation between barcode representations (normalized barcode counts) within the plasmid pool and infected cell pool indicates efficient lentiviral delivery of the pairwise gRNA library into cells. The horizontal dotted lines in the Bland-Altman plots indicate the 95% limits of agreement.

(C-D) High reproducibility for barcode representations between two biological replicates in cells cultured for 15-day (C), and 21-day (D) post-infection with the pairwise gRNA library. The horizontal dotted lines in the Bland-Altman plots indicate the 95% limits of agreement. The vertical dash line indicates the threshold of 100 raw barcode counts.

(E) The coefficient of variation (CV; defined as SD/mean of the fold changes of normalized barcode counts for 21-day versus 15-day cultured cells) was determined for the two biological replicates. Over 99.2% of pairwise gRNA combinations had a CV of <1 in the screen.

(F) OVCAR8-ADR-Cas9 cells infected with the barcoded pairwise gRNA library were cultured for 15 and 21 days. Barcode representations within the cell pools were quantified using Illumina HiSeq. The barcoded library vector uses hH1-gRNA-WT scaffold and hU6-gRNA-v1 scaffold in the first and second expression cassettes, respectively.

(G) A volcano plot for comparing the abundance changes of each barcoded gRNA combinations at day 21 versus day 15 post-infection. Hit combinations, DNMT1+PARP1 and FKBP1A+CDK2, are highlighted in blue and red, respectively. Data were collected from two biological replicates.

(H-J, M-N) Cell viability, determined by MTT assay, of the indicated gRNA-infected OVCAR8-ADR-Cas9 cells (H) and drug-treated OVCAR8-ADR cells (I, J, M, N). In (J and N), percentage of growth inhibition was calculated by comparing each drug-treated group to the untreated control. Drug synergy was measured by the Bliss Independent model and the HSA model. The growth-inhibitory effects brought by treatment with 8 μM of OLA and 1.2 μM of AZA (J), and 5 μM SEL and 0.5 μM SIR (N), were plotted as examples to illustrate, and the dash lines indicate the expected drug combination effects based on the Bliss Independent model. Data shown are mean±SD from biological replicates (n=3 in H; n=6 in I and J; n=8 in M and N).

(K, O) Colony formation assay of OLA- and/or AZA- (K), and SEL- and/or SIR- (O), treated OVCAR8-ADR cells. The colony numbers and areas were quantified. Data shown are mean±SD from biological replicates (n=3).

(L, P) Cell cycle analysis of OLA- and/or AZA- (K), and SEL- and/or SIR- (O), treated OVCAR8-ADR cells. The percentage of cells in each cell cycle phase was quantified. Data shown are mean±SD from biological replicates (n=3).

Statistical significance in H-P was analysed by one-way ANOVA with Tukey's post hoc test. *P<0.05, **P<0.01, and ****P<0.0001; ^(#)P<0.05 in J-L and N-O indicates the comparisons with the untreated control.

FIG. 14 . Growth-inhibitory effects brought by AZA and OLA, and SEL and SIR, on OVSAHO and KURAMOCHI cells

(A-B) Growth inhibition brought by the indicated drug treatments to OVSAHO (A) and KURAMOCHI (B) cells were measured by MTT assay, and was calculated by comparing each drug treatment to the untreated control. Drug synergy was measured by Bliss Independent model and HSA model. The dash line in the plots in the right panels indicates the expected drug combination effects based on the Bliss Independent model. Data are mean±SD from biological replicates (n=4). Statistical significance was analysed by one-way ANOVA with Tukey's post hoc test. *P<0.05; #P<0.05 indicates the comparisons with the untreated control.

FIG. 15 . A CRISPR-based dual-gene knockout screen identifies a drug combination that enhances protection against Parkinson's disease toxicity

(A) Distributions of barcode reads in the plasmid and infected SK-N-MC-Cas9 cell pools. 99.1% (7,499 out of 7,569) and 98.7% (7,467 out of 7,569) of all expected gRNA combinations was obtained in the plasmid and cell pools, respectively. Most barcoded gRNA combinations were detected within a 5-fold range from the mean barcode reads per combination (highlighted by the shaded areas).

(B) High correlation between barcode representations (normalized barcode counts) within the plasmid pool and infected cell pool indicates efficient lentiviral delivery of the pairwise gRNA library into cells.

(C) High correlation between barcode representations within cell pools cultured for 10 and 22 days indicates the CRISPR-mediated gene knockouts did not result in severe cell death.

(D-E) High reproducibility for barcode representations between two biological replicates in untreated (D) and rotenone-treated (E) cells. The dash lines in (D) indicate the threshold of 20 raw barcode counts. R is the Pearson correlation coefficient.

(F) SK-N-MC-Cas9 cells infected with the barcoded pairwise gRNA library were either treated with rotenone or remained untreated. Barcode representations within the cell pools were quantified using Illumina HiSeq.

(G) Lentiviral delivery of dual-gRNA expression constructs efficiently disrupt multiple target genes in SK-N-MC-Cas9 cells. Flow cytometry was used to measure the percentage of cell populations positive for GFP and RFP fluorescence at day 6 post-infection. Data are mean±SD, n=3 biological replicates.

(H) A volcano plot for comparing the abundance changes of each barcoded gRNA combinations in rotenone-treated versus untreated cell pools. Hit combination, HSP90B1+HDAC2, is highlighted in red. Data were collected from two biological replicates.

(I) Cell viability, determined by MTT assay, of the indicated sgRNA-infected SK-N-MC-Cas9 cells in the presence of rotenone. Data shown are mean±SD (n=4) from biological replicates, and data of left and right panels were obtained from the same experiments.

(J-K) Cell viability of the indicated drug-treated SK-N-MC cells (J) and iPSC-derived dopaminergic neurons (K) in the presence of rotenone, determined by MTT assay and DAPI uptake assay, respectively. Data shown in are mean±SD (n=9 in (J); n=3 in (K)) from biological replicates.

(L) Cell viability, determined by MTT assay, of the indicated drug-treated SK-N-MC cells in the presence of MPP⁺. Data shown are mean±SD (n=8) from biological replicates.

(M) Quantification of the number of rhabdomeres per ommatidium in wild-type and alpha-synuclein-expressing flies that were fed with the indicated drug(s). Combination of 17-DMAG and vorinostat restored the number of rhabdomeres per ommatidium in alpha-synuclein-expressing Drosophila eyes. Representative images showing the rhabdomeres of wild-type and alpha-synuclein-expressing flies that were fed with the indicated drug(s). Data are mean±SD from at least 100 ommatidia of 5-10 flies.

Statistical significance in (I-M) was analysed by one-way ANOVA with Tukey's post hoc test. *P<0.05, **P<0.01 and ****P<0.0001 represent significant differences between the indicated samples. In (I), ^(#)P<0.05, ^(##)P<0.01, ^(###)P<0.001, and ^(####)P<0.0001 indicates the comparisons with the respective no gRNA controls. Dash line indicates the expected drug combination effects based on the Bliss Independent model.

FIG. 16 . Engineered gRNA scaffold variants exhibit improved on-target and low off-target activities.

(A) Sequence of gRNA scaffold sequences used.

(B-C) OVCAR8-ADR cells harboring reporter constructs with on-target (B) and off-target (C) sites were infected with lentiviruses encoding wildtype or Opti-SpCas9. The editing efficiency of the gRNA scaffold variants was measured as the percentage of cells with depleted RFP fluorescence.

(D) Assessment of gRNA scaffold variants for efficient on-target editing with gRNAs targeting endogenous loci. The percentage of sites with indels was measured using a T7 endonuclease I (T7E1) assay. The ratio of the on-target activity of gRNA scaffold variants to the activity of scaffold was determined, and the median and interquartile range for the normalized percentage of indel formation are shown for the 5 loci tested. Each locus was measured three times.

(E) GUIDE-seq genome-wide specificity profiles for the panel of gRNA scaffold variants paired with the indicated gRNAs. Mismatched positions in off-target sites are colored, and GUIDE-seq read counts were used as a measure of the cleavage efficiency at a given site.

5. DETAILED DESCRIPTION

Combinatorial drug therapy targeting multiple pathways can limit the development of drug resistant phenotype in cancer cells since it is harder for the cells to activate multiple compensatory survival mechanisms.

This disclosure relates to systems and compositions that enables highly efficient, multiplexed genome editing and CRISPR screening. The engineered guide RNA scaffolds and promoters developed in this work enable three-way combinatorial CRISPR screens to be carried out based on a prior assembly method called CombiGEM-CRISPR, and can be used to improve genome editing efficiency in routine experiments and applications. High-throughput CRISPR screens from prior arts have only been able to study paired interactions between guide RNAs, and not those of greater complexity (such as interactions between three or more guide RNAs). The systematic screening of complex genetic interactions is enabled by the generation of engineered scaffolds and promoter sequences that can minimize possible lentiviral vector recombination due to long homologous sequences and permit use of the same pool of guide RNA oligos for building high-quality combinatorial guide RNA libraries.

Technically, the guide RNA scaffold sequences are engineered to minimize possible lentiviral vector recombination due to long homologous sequences, and the 3′ end of the promoter sequences of hH1 and mU6 are modified such that the same pool of gRNA oligos can be used for building the combinatorial guide RNA libraries. The engineered guide RNA scaffold and modified promoter sequences show higher or comparable activity for driving guide RNA expression when compared to their wild-type counterparts.

5.1 Design of CombiGEM-CRISPR v2.0

CombiGEM-CRISPR v2.0 toolkits include add-on designs on library vectors that enable only a single, reusable set of oligos to be synthesized for performing high-order combinatorial CRISPR screens. We and others have shown that CRISPR screens can be carried out via targeting two genes simultaneously using dual guide RNA (gRNA) expression cassettes (Chow et al., 2019; Du et al., 2017; Han et al., 2017; Najm et al., 2018; Shen et al., 2017; Wong et al., 2016a). Here we evaluated the extensibility of existing methods and other possible toolkits for assembling a three-way combinatorial gRNA library for screening (FIG. 1 ). Considering using an oligo synthesis-based approach to build a library with m_(a)×m_(b)×m_(c) combinations, the same number of gRNA protospacers-containing oligos (i.e., m_(a)×m_(b)×m_(c)) has to be first designed and synthesized to include all combinations and followed by sequential insertions of the promoter and scaffold sequences. The drawbacks are that (1) all the intermediate cloning steps require large-scale bacterial transformations for maintaining a high library coverage, which is technically more demanding than CombiGEM-CRISPR v2.0 method that only requires a large-scale transformation at the final assembly step, and (2) the rigid cloning framework does not permit post-assembly insertion of additional gRNAs for building higher-order libraries. The inflexible workflow also limits the reusability of oligos for building a more compact library for secondary screens. For example, if a pairwise gRNA library was constructed for identifying the core effectors to be included in a three-way gRNA library, building of the higher-order library requires new set of oligos to be synthesized for a complete re-assembly of libraries. Alternative library assembly strategies are through Gibson- (Gibson et al., 2009) or Golden-gate-(Engler et al., 2008) based methods, which require designing overlapping regions or complementary overhang of adjacent gRNA expression units for fusing multiple parts together. However, these methods also do not allow additional parts to be introduced to pre-existing barcoded libraries. Our CombiGEM-CRISPR v2.0 strategy provides a truly scalable solution that enables multiplicative assembly of additional barcoded gRNA expression units for extending from n to n+1 combinatorial CRISPR libraries (FIG. 2 ). Libraries can be also tailored and re-assembled from selected gRNAs by choosing from the suite of gRNAs stored in vectors for another screen or a secondary screen for higher resolution. In addition, the creation of barcodes that are unique for each assembled combination allows their rapid characterization to be performed via short-sequencing reads, which reduces the sequencing cost and potential errors generated via long reads. We therefore decided to take this approach to build three-way combinatorial gRNA libraries for screening applications.

Since previous CombiGEM toolkits were not directly adaptable for assembling three-way and even higher-order combinatorial gRNA libraries, here we further created a “one-set-fits-all” design such that building a n-way combinatorial CRISPR screening library of m guide RNAs using multiple gRNA expression cassettes always requires only m (instead of n×m) pairs of oligos to be synthesized. To ensure expression of three gRNAs in single cells, we assembled together the multiple gRNA expression cassettes in a single vector. Multiple promoters (including human U6, mouse U6, and human H1) (Adamson et al., 2016; Ma et al., 2014; Vidigal and Ventura, 2015) and modified gRNA scaffolds (Adamson et al., 2016; Briner et al., 2014; Dang et al., 2015; Grevet et al., 2018) were used in the expression cassettes (FIG. 6 ), which minimizes possible lentiviral vector recombination due to long homologous sequences. However, the use of multiple promoters requires multiple sets of oligos, and/or additional PCR and restriction enzyme digestion reactions, for building the different expression cassettes for library assembly. To allow researchers synthesizing and annealing only a single set of oligos as parts to build all possible higher-order combinations of gRNAs for multiplexed CRISPR screens, we performed sequence adaptation by modifying the 3′ end sequence of promoters to those that are complementary to the sticky ends of the annealed oligos, and these promoters expressed gRNAs and generated efficient gene knockouts (FIG. 6 ). These new standardized vector parts are useful for the flexible assembly of high-order combinatorial gRNA libraries and extensible combinatorial CRISPR screens.

In some embodiments, the promoters have sequences as shown below.

>Wild type Human U6 promoter: AGAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGG CTGTTAGAGAGATAATTAGAATTAATTTGACTGTAAACACAAAGATATTA GTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCAGT TTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAA AGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACC G Modified Mouse U6 promoter: GATCCGACGCCGCCATCTCTAGGCCCGCGCCGGCCCCCTCGCACAGACTT GTGGGAGAAGCTCGGCTACTCCCCTGCCCCGGTTAATTTGCATATAATAT TTCCTAGTAACTATAGAGGCTTAATGTGCGATAAAAGACAGATAATCTGT TCTTTTTAATACTAGCTACATTTTACATGATAGGCTTGGATTTCTATAAG AGATACAAATACTAAATTATTATTTTAAAAAACAGCACAAAAGGAAACTC ACCCTAACTGTAAAGTAATTGTGTGTTTTGAGACTATAAATATCCCTTGG AGAAAAGCCTT CACCG >Wild type Mouse U6 promoter (GeneBank: X06980.1) GATCCGACGCCGCCATCTCTAGGCCCGCGCCGGCCCCCTCGCACAGACTT GTGGGAGAAGCTCGGCTACTCCCCTGCCCCGGTTAATTTGCATATAATAT TTCCTAGTAACTATAGAGGCTTAATGTGCGATAAAAGACAGATAATCTGT TCTTTTTAATACTAGCTACATTTTACATGATAGGCTTGGATTTCTATAAG AGATACAAATACTAAATTATTATTTTAAAAAACAGCACAAAAGGAAACTC ACCCTAACTGTAAAGTAATTGTGTGTTTTGAGACTATAAATATCCCTTGG AGAAAAGCCTT >Modified Human H1 promoter: TTCGAACGCTGACGTCATCAACCCGCTCCAAGGAATCGCGGGCCCAGTGT CACTAGGCGGGAACACCCAGCGCGCGTGCGCCCTGGCAGGAAGATGGCTG TGAGGGACAGGGGAGTGGCGCCCTGCAATATTTGCATGTCGCTATGTGTT CTGGGAAATCACCATAAACGTGAAATGTCTTTGGATTTGGGAATCTTATA AGTTCTGTATGAGACCACTCTT CACCG >Wild type Human H1 promoter (GeneBank: X16612.1) TTCGAACGCTGACGTCATCAACCCGCTCCAAGGAATCGCGGGCCCAGTGT CACTAGGCGGGAACACCCAGCGCGCGTGCGCCCTGGCAGGAAGATGGCTG TGAGGGACAGGGGAGTGGCGCCCTGCAATATTTGCATGTCGCTATGTGTT CTGGGAAATCACCATAAACGTGAAATGTCTTTGGATTTGGGAATCTTATA AGTTCTGTATGAGACCACTCTT

5.2 Establishment of a CRISPR-Cas9-Based Multi-Gene Knockout System

We constructed a lentiviral combinatorial gRNA expression vector containing multiple gRNA expression cassettes to efficiently and simultaneously knock out three target genes (FIG. 3 ), and evaluated its functionality in human cells (OVCAR8-ADR) using gRNAs targeting the exonic regions of green (GFP), red (RFP), and blue (BFP) fluorescent protein reporter genes. Lentiviruses carrying a BFP reporter and the combinatorial gRNA units were generated to infect both the OVCAR8-ADR and OVCAR8-ADR-Cas9 cells stably expressing RFP and GFP reporters. Flow cytometry analysis was performed to confirm the effective generation of double- and triple-knockout of the reporter proteins (>81% and >74%, respectively) (FIG. 3 ). Similar knockout efficiencies were observed when wildtype (WT) or modified gRNA scaffolds were used. Our results indicate that the lentiviral vector can be used to deliver gRNAs to generate multi-gene knockouts, and this vector design was used for the combinatorial CRISPR-Cas9 screens in this study.

5.3 Three-Way Combinatorial CRISPR-Cas9 Screen for Synergistic Anti-Cancer Genetic Combinations

Combinatorial drug therapy targeting multiple pathways can limit the development of drug resistant phenotype in cancer cells since it is harder for the cells to activate multiple compensatory survival mechanisms (Bozic et al., 2013). We performed high-throughput studies to search for effective therapeutic combinations against high-grade serous ovarian cancer (HGSOC), the most prevalent subtype that contributes to two-third of all ovarian cancer deaths (Bowtell, 2010). With the CRISPR-based multi-gene knockout system described above, we applied CombiGEM-CRISPR v2.0 to assemble a high-coverage (99.8%) three-way combinatorial gRNA library (with 32×32×32 gRNAs=32,768 total combinations) (FIG. 4A-E). This library included 15 druggable protein-encoding genes (with 2 gRNAs per gene) that are commonly targeted in anti-cancer therapies and whose expressions were reported in OVCAR8-ADR, an established cell model of HGSOC (Baratta et al., 2015), and also other ovarian cancer cells based on the NCI-60 proteome database (Gholami et al., 2013) to demonstrate the feasibility of our approach (Table S2 and S3). To generate combinatorial gene knockouts at a high rate, we selected gRNAs with predicted high on-target (and low off-target) activities based on the Azimuth 2.0 model (Doench et al., 2016). We compared the on-target efficacy score and the indel generation efficiency of gRNAs, and observed that the on-target efficacy score largely predicts the efficiency of gRNAs in OVCAR8-ADR cells (FIG. 7A). We chose gRNAs that have on-target scores>0.64 based on the Azimuth 2.0 model, and most of them also have high frameshift generation rates analysed under the newly developed inDelphi and FORECasT models (FIG. 8 ) (Allen et al., 2018; Shen et al., 2018). Two non-targeting control gRNAs from the GeCKOv2 library (Shalem et al., 2014) that do not have on-target loci in the human genome were also included in the library as references.

TABLE S2 List of druggable genes included in the ovarian cancer study. Also included in the three-way combinatorial CRISPR-Cas9 Gene_ID Gene name Matching inhibitor drug screen ABCC1 Multidrug resistance-associated protein 1 Sulfinpyrazone ACAA1 3-ketoacyl-CoA thiolase, peroxisomal Trimetazidine AKT1 AKT serine/threonine kinase 1 MK-2206 ALDH2 Aldehyde dehydrogenase, mitochondrial Disulfiram APEX1 DNA-(apurinic or apyrimidinic site) lyase Lucanthone ATP1A1 Sodium/potassium-transporting ATPase Digoxin; Acetyldigitoxin; Deslanoside; subunit alpha-1 Ouabain CDK2 Cyclin dependent kinase 2 Hymenialdisine CDK4 Cyclin-dependent kinase 4 Palbociclib; Ribociclib; Abemaciclib Yes COMT Catechol O-methyltransferase Tolcapone; Entacapone CPT2 Carnitine O-palmitoyltransferase 2, Perhexiline mitochondrial CYP51A1 Lanosterol 14-alpha demethylase Itraconazole DHODH Dihydroorotate dehydrogenase (quinone), Leflunomide mitochondrial DNMT1 DNA (cytosine-5)-methyltransferase 1 5-azacytidine Yes EGFR Epidermal growth factor receptor Gefitinib; Erlotinib; Cetuximab; Lapatinib; Yes Panitumumab ERBB2 Receptor tyrosine-protein kinase erbB-2 Pertuzumab; Lapatinib; Trastuzumab; Afatinib Yes FASN Fatty acid synthase Cerulenin; Orlistat FDPS Farnesyl pyrophosphate synthase Pamidronic acid; Zoledronic acid; Alendronic acid; Ibandronate; Risedronic acid FGF2 Fibroblast growth factor 2 Pentosan Polysulfate Yes FGFR1 Fibroblast growth factor receptor 1 Regorafenib, Sorafenib; Lenvatinib FKBP1A Peptidyl-prolyl cis-trans isomerase FKBP1A Tacrolimus; Sirolimus GANAB Neutral alpha-glucosidase AB Miglitol GSR Glutathione reductase, mitochondrial Carmustine HDAC1 Histone deacetylase 1 Vorinostat; Panobinostat; CI-994; Romidepsin Yes HPRT1 Hypoxanthine-guanine phosphoribosyltransferase Azathioprine; Mercaptopurine IDE Insulin-degrading enzyme Bacitracin IKBKB Inhibitor of nuclear factor kappa-B kinase Auranofin Yes subunit beta IMPD-12 Inosine-5′-monophosphate dehydrogenase 2 Mycophenolate mofetil; Mycophenolic acid KDM4C Lysine demethylase 4C SD70 KDM6B Lysine demethylase 6B GSK-14 KEAP1 Kelch-like ECH-associated protein 1 Dimethyl fumarate M6PR Cation-dependent mannose-6-phosphate receptor Alglucosidase alfa MAP2K1 Dual specificity mitogen-activated Trametinib; Cobimetinib Yes protein kinase kinase 1 MAPK3 Mitogen-activated protein kinase 3 Sulindac METAP2 Methionine aminopeptidase 2 Nitroxoline MTOR Serine/threonine-protein kinase mTOR Everolimus; Temsirolimus; Sirolimus Yes NPC1L1 Niemann-Pick C1-like protein 1 Ezetimibe NR3C1 Glucocorticoid receptor Budesonide PARP1 Poly [ADP-ribose] polymerase 1 Olaparib; Rucaparib, Niraparib; Talazoparib PDGFRB Platelet-derived growth factor receptor beta Becaplermin; Sorafenib; Sunitinib; Pazopanib; Regorafenib PIK3C3 Phosphatidylinositol 3-kinase catalytic GDC-0941 Yes subunit type 3 POLA1 DNA polymerase alpha catalytic subunit Clofarabine; Fludarabine; Cladribine Yes PRDX5 Peroxiredoxin-5, mitochondrial Auranofin PSMB1 Proteasome subunit beta type-1 Bortezomib; Carfilzomib RRM1 Ribonucleoside-diphosphate reductase Hydroxyurea; Gemcitabine; Clofarabine; large subunit Fludarabine; Cladribine SLC12A4 Solute carrier family 12 member 4 Bumetanide SLC25A5 ADP/ATP translocase 2 Clodronic acid SOAT1 Sterol O-acyltransferase 1 Ezetimibe; Hesperetin TGFB1 Transforming growth factor beta 1 Hyaluronidase (Human Recombinant) Yes TOP1 DNA topoisomerase 1 Irinotecan; Topotecan; Lucanthone; Sodium Yes stibogluconate TUBA1A Tubulin alpha-1A chain Mebendazole Yes TYMS Thymidylate synthase Gemcitabine; 5-Fluorouracil; Raltitrexed; Yes Trimethoprim; Pemetrexed; Capecitabine; Trifluridine; Pralatrexate; Tegafur-uracil; Tegafur; Methotrexate VKORC1 Vitamin K epoxide reductase complex Phenindione; Dicoumarol; Warfarin; subunit 1 Phenprocoumon; Acenocoumarol

TABLE S3 List of ERNAs used in this study Also included in the On-target score Off-target three-way combinatorial gRNA ID gRNA target sequence (Azimuth2.0) rank CRISPR-Cas9- screen dummysg1 ATCGTTTCCGCTTAACGGCG Yes dummysg2 AAACGGTACGACAGCGTGTG Yes dummysg3 CCATCACCGATCGTGAGCCT ABCC1sg1 AAAATGTGATTGGCCCCAAG 0.6789 60 ABCC1sg2 CGTGTACTGGGACTACATGA 0.6664 62 ABCC1sg3 AGCCCCGGACAATCAACCTG 0.6773 83 ACAA1sg1 TCAATAGACAGTGTTCGTCG 0.7337  3 ACAA1sg2 TCTCTCGGCAGTCATGACCG 0.7808 23 ACAA1sg3 CTTGTCATCATGGACCGTGG 0.6923 27 AKT1sg1 CTCACCCAGTGACAACTCAG 0.6993 61 ATK1sg2 CCTGCACTCGGAGAAGAACG 0.6252 46 ATK1sg3 GAAGGTGCGTTCGATGACAG 0.6712 14 ALDH2sg1 CCCTGTGTGATGCGTCCATG 0.6699 14 ALDH2sg2 TGAAGAAGTCTCCGTCAATG 0.6996 29 ALDH2sg3 AGCCTTGGCAACTGGAAACG 0.66 17 APEX1sg1 ATGCCGTAAGAAACTTTGAG 0.735 28 APEX1sg2 ACTCCAGTCGTACCAGACCT 0.7174 74 APEC1sg3 GAGGTCTCCACACAGCACAA 0.7209 69 ATP1A1sg1 TGAGAAAATGAGCATAAATG 0.6891 12 ATP1A1sg2 TGGTATTGTTGTCTACACTG 0.8027 40 ATP1A1sg3 CCTGCCTCTTACCGTGACAG 0.659 14 CDK2sg1 TGTTCGTACTTACACCCATG 0.7385 17 CDK2sg2 ATCTGCTTATTAACACAGAG 0.6812 40 CDK2sg3 TGAGAAGCATTACCTTGATG 0.6625 50 CDK4sg1 CCAGATGGCACTTACACCCG 0.6632  9 CDK4sg2 GTCCACATATGGAACACCTG 0.6728 36 Yes CDK4sg3 GTCTACATGCTCAAACACCA 0.7065 51 Yes COMTsg1 CTGGGACGCTCCAACCACAA 0.7352  6 COMTsg2 ACTGTGCCGCCATCACCCAG 0.7332  8 COMTsg3 ACCCTGCACAGGCAAGATCG 0.6727 42 SPT2sg1 GATAGGTACATATCAAACCA 0.7621 17 CPT2sg2 CACCCCAAGAGTGCTCAAAG 0.6732 18 CPT2sg3 TGGGAACATTGTGAGCCCCT 0.6515 30 CYP51A1sg1 GAATGTACGTACCACCCCTG 0.711 14 CYP51A1sg2 TACGATGTGCCTAATCCAGT 0.6428  6 CYP51A1sg3 TCAACTACTAGTGCTTGGAT 0.6033 15 DHODHsg1 GTGACTCCAAAACCTCAGGA 0.6721 22 DHODHsg2 TGGAGGATTTGACAAGCATG 0.6648 61 DHODHsg3 ATAGAAACGCTCATCTCCCG 0.666 62 DNMT1sg1 GATTTCTGATGAAAAAGACG 0.7305 76 Yes DNMT1sg2 CACCTGTGTCCCATCGACAC 0.6463 11 Yes DNMT1sg3 AAGAATCGCATCTCTTGGGT 0.643 66 EGFRsg1 GAGAACCTAGAAATCATACG 0.7897 59 Yes EGFRsg2 TGTCACCACATAATTACCTG 0.7371 28 Yes EGFRsg3 GTGGAGCCTCTTACACCCAG 0.7258 29 ERBB2sg1 CAGAACCTGCAAGTAATCCG 0.7032 46 Yes ERBB2sg2 AACTACCTTTCTACGGACGT 0.7025  1 Yes ERBB2sg3 TCATCGCTCACAACCAAGTG 0.6636 21 FASNsg1 CGAGACCCCGAGACACTCGT 0.7338 30 FASNsg2 GATGTATTCAAATGACTCAG 0.7027 68 FASNsg3 CATCTCCCCACTCATCAAGT 0.6486 64 FDPSsg1 ATTGGAGGCAAGTATAACCG 0.7288  2 FDPSsg2 GATTCATCCCTTACCCGCCG 0.6907 57 FDPSsg3 CTGGTGCCAAGCGTGGACAG 0.6761 50 FGF2sg1 CGGCTGTACTGCAAAAACGG 0.7347 84 Yes FGF2sg2 TTCACGGATGGGTGTCTCCG 0.6635 18 Yes FGF2sg3 CGGACAGAAGAGCGGCCGAG 0.6363 74 FGFR1sg1 ACCCAACCGTGTGACCAAAG 0.7016 30 FGFR1sg2 GTTGCCCGCCAACAAAACAG 0.6998 24 FGFR1sg3 AAGTATTATTACCTGTCCCG 0.6787 42 FKBP1Asg1 GGCAAGCAGGAGGTGATCCG 0.6739 24 FKBP1Asg2 CCACTACTCACCGTCTCCTG 0.6674 15 FKBP1Asg3 ACCGGTGTAGTGCACCACGC 0.6372 14 GANABsg1 TGGCAAGCGGTATTTCACCT 0.7091 74 GANABsg2 ACATCTGGTACACGGTATCG 0.6768 53 GANABsg3 TGACACTAAGCAAAAGACTT 0.6671 45 GSRsg1 CTATCAAAACAATCTCACCA 0.7093 59 GSRsg2 CACATCCTGATCGCCACAGG 0.6758 48 GSRsg3 TATTTGCCAATAGGTCAAGG 0.6257 22 HDAC1sg1 CATCCGTCCAGATAACATGT 0.7267 13 Yes HDAC1sg2 AGTGCGGTGGTCTTACAGTG 0.6952 62 Yes HDAC1sg3 GAAACTTAATAAGCAGCAGA 0.669 48 HPRT1sg1 ACTAGAATGACCAGTCAACA 0.688 24 HPRT1sg2 CTGTCCATAATTAGTCCATG 0.6695 12 HPRT1sg3 GCCCCCCTTGAGCACACAGA 0.6511 34 IDEsg1 ATCTTAGATGTATAGCCCCG 0.7099 41 IDEsg2 TATACCGGATGAAGTCATCA 0.6852 61 IDEsg3 AAGACAAGCGAGAATATCGA 0.6616 39 IKBKBsg1 TTTGCAGGCATTCAAAAGTG 0.7037 75 YeS IKBKBsg2 GCCATGGAGTACTGCCAAGG 0.6934 61 Yes IKBKBsg3 TATTGACCTAGGATATGCCA 0.6209 52 IMPDH2sg1 GAGAAAATCAATGTCCCTGG 0.6938 19 IMPDH2sg2 CATCCCGCACGCGATCCTTG 0.6571 86 IMPDH2sg3 ATTCAGGTGTACAGTTGTGG 0.6544 17 KDM4Csg1 GCAAGAGTATAATGCAACAG 0.6983 38 KDM4Csg2 AGCTATTTCTCTCTCCACTG 0.675 43 KDM4Csg3 GGTCATCTGTGACTGAGTCG 0.6632 27 KDM6Bsg1 GAGTCAGGGGTACAAGAGGT 0.6839 53 KDM6Bsg2 GCAGTCGGAAACCGTTCTTG 0.6837 20 KDM6Bsg3 GACAAAAGTACTGTTATCGG 0.6835 39 KEAP1sg1 TTGGCATCATGAACGAGCTG 0.6626 90 KEAP1sg2 TGACAGCACCGTTCATGACG 0.6555 14 KEAP1sg3 CTGTCGGAAGTAGCCGCCCG 0.6544 81 M6PRsg1 GATGAATATGACAACCACTG 0.7696  9 M6PRsg2 CTGCAATCGACACACCCTAG 0.7619  1 M6PRsg3 AGATGTATGTGTCTGAACCC 0.6995  7 MAP2K1sg1 CATCCTAGTCAACTCCCGTG 0.7356 11 Yes MAP2K1sg2 GGGCACAAGGTCCTACATGT 0.6946  6 Yes MAP2K1sg3 GCAGCAGCGAAAGCGCCTTG 0.6905  5 MAPK3sg1 AGTACGTCTGATGTTCGAAG 0.6876 22 MAPK3sg2 GCAGTTGCAGTACATCGGCG 0.6814  6 MAPK3sg3 TCTGACCTTAAGGTCGCAGG 0.6566 48 METAP2sg1 TCTTGCTACTTCATCCACTG 0.7212 25 METAP2sg2 TCGTCTGTGTGATGTTGGTG 0.6636 94 METAP2sg3 TTATTGAGAGAACATCCAGT 0.6598 56 MTORsg1 TCAGGAAATGATCCGCACAG 0.7812 41 Yes MTORsg2 GGTGATGGCCTGGACAACCA 0.6918 61 Yes MTORsg3 CAGCTCGTTAAGGATCAACA 0.6888 65 NPC1L1sg1 AGAACTCACTACGGACCCCG 0.7107  2 NPC1L1sg2 GGAGGAGCGGATACCCAAGT 0.7024 13 NPC1L1sg3 CTTCGGGCGACCATACCTGG 0.7005 12 NR3C1sg1 CATCGAACTCTGCACCCCTG 0.6933 31 NR3C1sg2 TAGAAAAAACTGTTCGACCA 0.6761  5 NR3C1sg3 TTAGTGTCCGGTAAAATGAG 0.6516 50 PARP1sg1 CGATGCCTATTACTGCACTG 0.7889 59 PARP1sg2 TACCGATCACCGTACCCACA 0.6616  2 PARPsg2 AACTCGGGGGGAAGTTGACG 0.6548 30 PDGFRBsg1 GACTAACGTGACGTACTGGG 0.7311 46 PDGFRBsg2 TGTGGTAAGGCATATCCAAG 0.7156 22 PDGFRBsg3 CTCCCGTGTCTAGCCCAGTG 0.6855 42 PIK3C3sg1 TAACTTACCATAGACATCTG 0.6701 59 Yes PIK3C3sg2 AGCCTGCAAAAACTCAACAC 0.6679 13 Yes PIK3C3sg3 TCCCTTGGCGAAACATGCTA 0.6611 43 POLA1sg1 CATGACACAACAGCTCACAT 0.7397 27 Yes POLA1sg2 CGACCTATCTTGGACCAGTG 0.7062 90 Yes POLA1sg3 AAGCACGCAATAAAGACCAG 0.6528 47 PRDX5sg1 CCTCACCTTGGAACATCCAG 0.6932 29 PRDX5sg2 TCAGCGGGCTATATACTCGT 0.6808  7 PRDX5sg3 AGCAGTGGAGGTGTTTGAAG 0.6629 59 PSMB1sg1 TATGTTTACAACATCATCGG 0.6656 13 PSMB1sg2 ATAATAAGGCCATGACTACG 0.6502 33 PSMB1sg3 AAAGGGCCCGCGGCTCTGTG 0.6371 76 RRM1sg1 CCTACCTAGAAAGTTGTGGG 0.7591 34 RRM1sg2 CTTGTACCCCAATTCCAATG 0.7264 19 RRM1sg3 TGGCAAACACTCTCCCATGG 0.7255 32 SLC12a4sg1 TCATGATCTCTCGTTCACTG 0.7057 25 SLC12a4sg2 AGCTACACCAACCTCACCCA 0.6965 28 SLC12a4sg3 CAGTGATAGTACTTGAACCG 0.6943 55 SLC25ASsg1 GGGTACGGGCAAAATCAAGA 0.7068 33 SLC25ASsg2 GTCATAGATACCGAAGTAGG 0.6741 18 SLC25ASsg3 GGAGTTCTGTCCTTCTGGCG 0.6636 11 SOAT1sg1 TTTGATATTCCGAAACAAGG 0.715 11 SOAT1sg2 ATTACCTGGGATAGCTGTCA 0.6625 60 SOAT1sg3 TCAGCATCATTAGATAATGG 0.662 16 TGFB1sg1 CTAATGGTGGAAACCCACAA 0.8801 54 Yes TGFB1sg2 GGTGAAGCGGAAGCGCATCG 0.7133 62 Yes TGFB1sg3 TTGATGTCACCGGAGTTGTG 0.6694 27 TOP1sg1 AGAAATACGAGACTGCTCGG 0.7785 81 Yes TOP1sg2 GCTATCTTGAAGGCATCAAG 0.6825 39 Yes TOP1sg3 ACTCACTCATCCTCATCTCG 0.6575 16 TUBA1Asg1 CTGTGATAAGTTGCTCAGGG 0.7492 23 Yes TUBA1Asg2 GAGACGTTCCATGAGCAGCG 0.7489 49 Yes TUBA1Asg3 CAGGTTCTTCAGTGAGACGG 0.665 32 TYMSsg2 ATGTGCGCTTGGAATCCAAG 0.7583  9 Yes TYMSsg3 ACCAAACGTGTGTTCTGGAA 0.63 14 TYMSsg3 CTGCATGCCGAATACCGACA 0.6611 50 Yes VKORC1sg1 GACGCGCGAACAGCTGATGG 0.6646 10 VKORC1sg2 ATATGCTGTTGGATTGATTG 0.6539  8 VKORC1sg3 GCTCAGCAGCATCAGGACAG 0.6408 41

We then conducted a pooled screen to isolate three-way gRNA combinations that modulate OVCAR8-ADR growth (FIG. 4F). Barcode abundances between day 15 and day 26 groups were compared to yield log₂ values as a measure of cell growth. Based on the genetic screen data, 3 (out of 455) three-way gene combinations had a mean log₂ ratios of <−1 (based on data obtained from two biological replicates with at least 50% fewer barcode counts in day 26-versus day 15-cultured cells) and a GI₃ score of <−0.2 (FIG. 4G and Table S4). These three-way combinations (targeting DNMT1+POLA1+EGFR or ERBB2, as well as CDK4+MAP2K1+POLA1) also showed significantly different growth-modulatory effects from their respective singles and pairwise combinations (FIG. 4H and Table S4). Because they showed strong growth inhibitory effects and strong synergistic genetic interactions, the three combinations were selected for further characterization. Their growth inhibition effects (reduced by 51.4 to 88.4% for the six tested gRNA combinations for DNMT1+POLA1+EGFR or ERBB2, and reduced by 50.5% and 54.9% for the two tested gRNA combinations for CDK4+MAP2K1+POLA1) were further confirmed by individual non-pooled assays and were not false positives that are caused by excessive DNA double stranded breaks generated by CRISPR-Cas9 (Aguirre et al., 2016; Munoz et al., 2016) because simultaneous targeting of three safe harbour loci did not result in strong growth arrest (FIGS. 4I, 7C and 9 ). In addition, the DNA copy number of DNMT1, POLA1, EGFR, ERBB2, CDK4, and MAP2K1 loci are not largely amplified in OVCAR8-ADR's genome based on the analysis using CellMiner (Reinhold et al., 2012).

TABLE S4 Comparison of three-way combinations with their respective pairwise combinations and singles mean log2 FC Dunnett test adjusted p-value A B C A + B A − C B + C A + B + C A vs A + B + C B vs A + B + C DNMT1_EGFR_POLA1 −0.27582 −0.25302 −0.45694 −0.47204 −0.58237 −0.6208 −1.12916 1.68575E−05 1.23229E−05 DNMT1_POLA1_ERBB2 −0.27582 −0.45694 −0.30289 −0.58237 −0.5251 −0.67235 −1.157

7 8.06438E−06 0.000979852 CDK4_MAP2K1_POLA1 −0.24531 −0.09528 −0.45

94 −0.07834 −0.6393 −0.6668 −1.05434 1.79325E−06 6.17188E−09 DNMT1_MAP2K1_POLA1 −0.27582 −0.09528 −0.45

94 −0.49617 −0.58237 −0.6668 −1.0197 7.56295E−05 6.79765E−07 CDK4_EGFR_MAP2K1 −0.24531 −0.2

302 −0.09528 −0.22505 −0.07834 −0.26597 −0.5581 0.143766687 0.163804785 ERBB2_MAP2K1_POLA1 −0.30289 −0.09528 −0.45694 −0.31148 −0.67235 −0.6668 −0.97996 0.000194702 9.4614E−07 CDK4_MAP2K1_MTOR −0.24531 −0.09528 −0.71279 −0.07834 −0.89932 −0.82537 −1.07497 0.000142157 3.00538E−06 DNMT1_FRBB2_FGF2 −0.27582 −0.30289 −0.05524 −0.5251 −0.33702 −0.3165 −0.61683 0.020636044 0.035969877 CDK4_EGFR_POLA1 −0.24531 −0.2

302 −0.45

94 −0.22505 −0.6393 −0.6208 −0.87853 0.002362653 0.002390339 CDK4_POLA1_TYMS −0.24531 −0.45694 −0.56

99 −0.6393 −0.59996 −0.99179 −1.21096 6.39159E−06 −0.000731016 CDK4_DNMT1_MTOR −0.24531 −0.27582 −0.71279 −0.29118 −0.89932 −0.78924 −1.14626 1.73973E−05 2.0496E−05 MAP2K1_POLA1_TUBA1A −0.09528 −0.45694 −0.25322 −0.66

8 −0.39044 −0.83211 −0.89524 5.42402E−05 0.070563059 CDK4_MAP2K1_TGFB1 −0.24531 −0.09528 −0.29065 −0.07834 −0.21676 −0.28856 −0.49914 0.528462646 0.094149343 DNMT1_POLA1_FGF2 −0.27582 −0.45694 −0.05524 −0.58237 −0.33702 −0.69009 −0.92057 0.000600146 0.03278394 M

OR_POLA1_FGF2 −0.71279 −0.45694 −0.05524 −1.11793 −0.82289 −0.69009 −1.34817 0.048878655 0.001585369 EGFR_ERBB2_FGF2 −0.26302 −0.30289 −0.05524 −0.54353 −0.30212 −0.3165 −0.53584 0.150419204 0.270462917 DNMT1_EGFR_FGF2 −0.27582 −0.2

302 −0.05524 −0.47204 −0.33702 −0.30212 −0.53054 0.212690145 0.172560015 DNMT1_FGF2_

GFB1 −0.27582 −0.05524 −0.29065 −0.33702 −0.34998 −0.24625 −0.55262 0.202825449 0.001777442 CDK4_EGFR_FGF2 −0.24531 −0.2

302 −0.05524 −0.22505 −0.15718 −0.30212 −0.46814 0.371902465 0.427368762 IKBKB_POLA1_TYMS −0.35773 −0.45694 −0.56399 −0.78623 −0.59343 −0.99179 −1.27533 5.62415E−07 2.57633E−05 FGFR_IKBKB_MTOR −0.26302 −0.35773 −0.71279 −0.37936 −0.82607 −0.77193 −1.1035 1.2411E−05 0.000113468 HDAC1_FGF2_TGFB1 −0.43459 −0.05524 −0.29065 −0.31779 −0.25654 −0.24625 −0.5966 0.751974137 0.000834327 DNMT1_ERBB2_MTOR −0.27582 −0.30289 −0.71279 −0.5251 −0.78924 −0.96817 −1.15868 1.33791E−05 2.03975E−05 MAP2K1_MTOR_IYMS −0.09528 −0.71279 −0.56

99 −0.82537 −0.71457 −1.0865 −1.33839 2.47173E−09 0.008968971 DNMT1_HDAC1_PIK3C3 −0.27582 −0.43459 −0.52951 −0.45571 −0.52531 −0.60726 −0.89332 3.02539E−05 0.00368773 ERBB2_MAP2K1_TUBA1A −0.30289 −0.09528 −0.25322 −0.31148 −0.55315 −0.39044 −0.59858 0.224633185 0.008003891 CDK4_ERBB2_POLA1 −0.24531 −0.30289 −0.45594 −0.40617 −0.6393 −0.67235 −0.84669 0.003743327 0.007318279 DNMT1_HDAC1_MAP2K1 −0.27582 −0.43459 −0.09528 −0.45571 −0.49617 −0.36008 −0.8339 0.000596059 0.027392423 EGFR_MAP2K1_POLA1 −0.26302 −0.09528 −0.45694 −0.26597 −0.6208 −0.6668 −0.83284 0.004286978 0.000113699 CDK4

MAP2K1

TUBA1A −0.24531 −0.09528 −0.25322 −0.07834 −0.40998 −0.39044 −0.53792 0.204616635 0.013084515 CDK4_IKBKB_MAP2K1 −0.24531 −0.35773 −0.09528 −0.3719 −0.07834 −0.25507 −0.40099 0.648294018 0.998640627 EGFR_MTOR_FGF2 −0.26302 −0.71279 −0.05524 −0.82607 −0.30212 −0.82289 −0.98555 0.001093007 0.566237444 CDK4_HDAC1_TGFB1 −0.24531 −0.43459 −0.29065 −0.37949 −0.21676 −0.25654 −0.55846 0.220578811 0.933499918 EGFR_HDAC1_FGF2 −0.26302 −0.43459 −0.05524 −0.45467 −0.30212 −0.31779 −0.62425 0.039691482 0.549656088 ERBB2_MAP2K1_TGFB1 −0.30289 −0.09528 −0.29065 −0.31148 −0.26734 −0.28856 −0.48749 0.570854335 0.023184407 POLA1_TUBA1A_FGF2 −0.45694 −0.25322 −0.05524 −0.83211 −0.69009 −0.69614 −1.03826 0.011622324 0.000145859 DNMT1_TYMS_FGF2 −0.27582 −0.55899 −0.05524 −0.69239 −0.33702 −0.61126 −0.78837 0.001332362 0.436324069 DNMT1_EGFR_ERBB2 −0.27582 −0.2

302 −0.30289 −0.47204 −0.5251 −0.54353 −0.69962 0.023545587 0.018160585 EGFR_IKBKB_TGFB1 −0.26302 −0.35773 −0.29065 −0.37936 −0.23667 −0.35915 −0.55022 0.228039641 0.620263102 EGFR_MAP2K1_MTOR −0.26302 −0.09528 −0.71279 −0.26597 −0.82607 −0.82537 −0.96433 0.005880513 0.000388782 DNMT1_POLA1_TUBA1A −0.27582 −0.45694 −0.25322 −0.58237 −0.59024 −0.83211 −0.98267 0.000538501 0.022492505 DNMT1_MAP2K1_FGF2 −0.27582 −0.09528 −0.05524 −0.49617 −0.33702 −0.31266 −0.44963 0.5

9671328 0.021023094 MAP2K1_POLA1_PIK3C3 −0.09528 −0.45694 −0.52951 −0.6668 −0.54595 −0.7048 −1.056 2.03089E−06 0.008159283 CDK4_ERBB2_FGF2 −0.24531 −0.30289 −0.05524 −0.40617 −0.15718 −0.3165 −0.41777 0.593253276 0.871088553 DNMT1_TUBA1A_FGF2 −0.27582 −0.25322 −0.05524 −0.59024 −0.33702 −0.69614 −0.82753 0.00169640

0.000965186 CDK4_DNMT1_FGF2 −0.24531 −0.27582 −0.05524 −0.29118 −0.15718 −0.33702 −0.43472 0.424982884 0.578899932 DNMT1_IKBKB_POLA1 −0.27582 −0.35773 −0.45594 −0.39718 −0.58237 −0.78623 −0.91427 0.000674911 0.003607117 MAP2K1_TUBA1A_TYMS −0.09528 −0.25322 −0.56899 −0.39044 −0.71457 −0.86356 −0.81521 2.17493E−06 0.000299208 HDAC1_MAP2K1_TGFB1 −0.43459 −0.09528 −0.29065 −0.36008 −0.25654 −0.28856 −0.56534 0.933687096 0.027556107 DNMT1_MTOR_MAP2K1 −0.27582 −0.71279 −0.09528 −0.78924 −0.49617 −0.82537 −1.04864 0.000146544 0.286373784 CDK4_DNMT1_IKRKB −0.24531 −0.27582 −0.35773 −0.29118 −0.3719 −0.39718 −0.48741 0.

00369163 0.295097681 EGFR_IKBKB_TUBA1A −0.26302 −0.35773 −0.25322 −0.3793

−0.60402 −0.49372 −0.79833 0.002671164 0.018290329 ERBB2_HDAC1_MAP2K1 −0.30289 −0.43459 −0.09

28 −0.41417 −0.31148 −0.36008 −0.57669 0.226112688 0.841239461 DNMT1_IKBKB_FGF2 −0.27582 −0.35773 −0.05524 −0.39718 −0.33702 −0.27441 −0.52158 0.173518014 0.5626546 POLA1_FGF2_PIK3C3 −0.45694 −0.05524 −0.52951 −0.69009 −0.7048 −0.58806 −1.045 0.010085071 4.35605E−07 ERBB2_POLA1_MTOR −0.30289 −0.45694 −0.71279 −0.67235 −0.96817 −1.11793 −1.25022 9.55576E−05 0.002507028 POLA1_FGF2_TGFB1 −0.45694 −0.05524 −0.29065 −0.69009 −0.8014

−0.24625 −0.80404 0.275910666 0.000402452 EGFR_FGF2_TGFB1 −0.26302 −0.05524 −0.29065 −0.30212 −0.23667 −0.24625 −0.41373 0.792933148 0.048117151 ERBB2_TYMS_TGFB1 −0.30289 −0.56899 −0.29065 −0.44854 −0.26734 −0.56701 −0.6894 0.032948211 0.020088785 DNMT1_POLA1_PIK3C3 −0.27582 −0.45694 −0.52951 −0.58237 −0.52531 −0.7048 −0.93003 0.003648714 0.075985702 EGFR_MAP2K1_TUBA1A −0.26302 −0.09528 −0.25322 −0.26597 −0.60402 −0.39044 −0.51588 0.441024411 0.055469074 CDK4_DNMT1_TOP1 −0.24531 −0.27582 −1.04454 −0.29118 −0.88189 −0.92996 −1.15025 4.41689E−06 5.28648E−06 EGFR_FGF2_PIK3C3 −0.26302 −0.05524 −0.52951 −0.30212 −0.56261 −0.58806 −0.66465 0.049844364 0.000448985 ERBB2_IKBKB_MAP2K1 −0.30289 −0.35773 −0.09528 −0.25115 −0.31148 −0.25507 −0.4827 0.578906006 0.864738713 ERBB2_POLA1_HGF2 −0.30289 −0.45694 −0.05524 −0.67235 −0.3165 −0.69009 −0.80404 0.006158122 0.134635799 DNMT1_HDAC1_IKBKB −0.27582 −0.43459 −0.35773 −0.45571 −0.39718 −0.43998 −0.64277 0.02585111b 0.413111828 EGFR_ERBB2_POLA1 −0.26302 −0.30289 −0.45694 −0.54353 −0.6208 −0.67235 −0.81062 0.008520223 0.015630324 ERBB2_IKBKB_FGF2 −0.30289 −0.35773 −0.05524 −0.25115 −0.3165 −0.27441 −0.48433 0.466973252 0.799377158 CDK4_HDAC1_FGF2 −0.24531 −0.43459 −0.05524 −0.37949 −0.15718 −0.31779 −0.39947 0.803315604 0.999863397 CDK4_MTOR_PIK3C3 −0.24531 −0.71279 −0.52951 −0.89932 −0.44216 −1.25268 −1.30511 1.13615E−05 0.0400936 EGFR_IKBKB_MAP2K1 −0.26302 −0.35773

.09528

.37936 0.26597 0.25507

.42983 0.64316491 0.987370635 CDK4_EGFR_IGFB1 −0.24531 −0.26302 −0.29065 −0.22505 −0.21676 −0.23667 −0.32004 0.993600852 0.998260113 CDK4_DNM

1_HDAC1 −0.24531 −0.27582 −0.43459 −0.29118 −0.37949 −0.45571 −0.52938 0.163117213 0.231192581 DNMT1_MAP2K1_TGFB1 −0.27582 −0.09528 −3.29065 −0.49617 −0.34998 −0.28856 −0.58947 0.131924639 0.004015538 DNMT1_LRBB2_TUBA1A −0.27582 −0.30289 −0.25322 −0.5251 −0.59024 −0.55315 −0.69503 0.02485

157 0.037713308

KBKB_POLA1_TUBA1A −0.35773 −0.45694 −0.25322 −0.78623 −0.49372 −0.83211 −0.99141 0.001210804 0.013339265 MAP2K

_POLA1_FGF2 −0.09528 −0.45694 −0.05524 −0.6668 −0.31266 −0.69009 −0.58619 0.007021954 0.909203172 ERBB2_HDAC1_IKBKB −0.30289 −0.43459 −0.35773 −0.41417 −0.25115 −0.43998 −0.57262 0.099135295 0.729141861 DNMT1_EGFR_TUBA1A −0.27582 −0.26302 −0.25322 −0.47204 −0.59024 −0.60402 −0.67926 0.0478958

6 0.038228411 EGFR_POLA1_PIK3C3 −0.26302 −0.45694 −0.52951 −0.6208 −0.56261 −0.7048 −0.94949 0.001578442 0.05205824 DNMT1_MTOR_TYMS −0.27582 −0.71279 −0.56899 −0.78924 −0.69239 −1.0865 −1.20247 2.77006E−06 0.047618515 HDAC1_IKBKB_TYMS −0.43459 −0.35773 −0.56899 −0.43998 −0.74076 −0.59343 −0.89491 0.003522734 0.00032417 EGFR_POLA1_TUBA1A −0.26302 −0.45694 −0.25322 −0.6208 −0.60402 −0.83211 −0.89107 0.007377139 0.130247391 CDK4_IKBKB_FGF2 −0.24531 −0.35773 −0.05524 −0.3719 −0.15718 −0.27441 −0.31524 0.981012104 0.998270315 CDK4_DNM

1_IGFB1 −0.24531 −0.27582 −0.29065 −0.29118 −0.21676 −0.34998 −0.38848 0.863534122 0.942145741 ERBB2_HDAC1_TYMS −0.30289 −0.43459 −0.56899 −0.41417 −0.44854 −0.74076 −0.83673 0.00

84304 0.02371194 PO

A1_

UBA1A_TYMS −0.45694 −0.25322 −0.56899 −0.83211 −0.99179 −0.86356 −1.19333 0.000728391 3.82

E−06 CDK4_EGFR_ERBB2 −0.24531 −0.26302 −0.30289 −0.22505 −0.40617 −0.54353 −0.57863 0.090500859 0.103530522 HDAC1_MAP2K1_TUBA1A −0.43459 −0.09528 −0.25322 −0.36008 −0.48481 −0.39044 −0.61428 0.73

81637 0.006494276 EGFR_ERBB2_TUBA1A −0.26302 −0.30289 −0.25322 −0.54353 −0.60402 −0.55315 −0.696 0.039751792 0.069748375 HDAC1_MAP2K1_MTOR −0.43459 −0.09528 −0.71279 −0.36008 −1.00956 −0.82537 −1.04751 0.0113238 1.84014E−05

KBKB_FGF2_TGFB1 −0.35773 −0.05524 −0.29065 −0.27441 −0.35915 −0.24625 −0.39099 0.99988379 0.072112801 EGFR

TYMS

FG

2 −0.2

302 −0.56899 −0.05524 −0.83951 −0.30212 −0.61126 −0.6763 0.01401285 0.939538474 HDAC1_POLA1_TUBA1A −0.43459 −0.45694 −0.25322 −0.98968 −0.48481 −0.83211 −1.04635 0.00751379 0.013380499 CDK4_HDAC1_MAP2K1 −0.24531 −0.43459 −0.09528 −0.37949 −0.07834 −0.36008 −0.38472 0.892659596 0.999283118 LRBB2_P

K3C3_

−0.30289 −0.52951 −0.29065 −0.50956 −0.26734 −0.43419 −0.57865 0.241

76298 0.999131863

GFR_POLA1_FGF2 −0.26302 −0.45694 −0.05524 −0.6208 −0.30212 −0.69009 −0.7293 0.01801824 0.369691504 MAP2K1_TUBA1A_TGFB1 −0.09528 −0.25322 −0.29065 −0.39044 −0.28856 −0.43878 −0.45636 0.08803125 0.584204221 ERBB2_TYMS_FGF2 −0.30289 −0.56899 −0.05524 −0.44854 −0.3165 −0.61126 −0.68892 0.018295767 0.8960647 MTOR_TUBA1A_TYMS −0.71279 −0.25322 −0.56899 −1.01377 −1.0865 −0.86356 −1.35739 0.006196109 8.02196E−08 ERBB2_MAP2K1_FGF2 −0.30289 −0.09528 −0.05524 −0.31148 −0.3165 −0.312

6 −0.38919 0.959404452 0.085215136 EGFR_IKBKB_POLA1 −0.26302 −0.35773 −0.45694 −0.37936 −0.6208 −0.78623 −0.81823 0.007108278 0.034058026 EGFR_HDAC1_MAP2K1 −0.26302 −0.43459 −0.09528 −0.45467 −0.26597 −0.36008 −0.46923 0.478277516 0.999846796 MAP2K

_TUBA1A_FGF2 −0.09528 −0.25322 −0.05524 −0.39044 −0.31266 −0.69614 −0.55751 0.0192887

1 0.217566258 CDK4_FGF2_

GFB1 −0.24531 −0.05524 −0.29065 −0.15718 −0.21676 −0.

4625 −0.2569 0.999999747 0.441920603 HDAC1_IKBKB_MAP2K1 −0.43459 −0.35773 −0.09528 −0.43998 −0.36008 −0.25507 −0.48256 0.998676835 0.85249117 IKBKB_MAP2K1_MTOR −0.35773 −0.09528 −0.71279 −0.25507 −0.77193 −0.82537 −0.94717 0.009667226 7.46209E−05 DNMT1_MTOR_FGF2 −0.27582 −0.71279 −0.05524 −0.78924 −0.33702 −0.82289 −0.86216 0.004856976 0.921401624 DNMT1_TYMS_TGFB1 −0.27582 −0.56899 −0.29065 −0.69239 −0.34998 −0.56791 −0.74618 0.012921765 0.745197905 ERBB2_IKBKB_TUBA1A −0.30289 −0.35773 −0.25322 −0.25115 −0.55315 −0.49372 −0.67366 0.051551322 0.131059049 POLA

_TUBA1A_IGFB1 −0.45694 −0.25322 −0.29065 −0.83211 −0.80145 −0.43878 −0.88506 0.162935605 0.009921379 EGFR_MTOR_TGFB1 −0.26302 −0.71279 −0.29065 −0.82607 −0.23667 −0.9

103 −0.93586 0.006721236 0.794669484 MAP2K

_TYMS_FGF2 −0.09523 −0.56899 −0.05524 −0.71457 −0.31266 −0.61126 −0.64305 6.39594E−05 0.982319193 CDK4_IKBKB_MTOR −0.24531 −0.35773 −0.71279 −0.3719 −0.89932 −0.77193 −1.01825 0.00062951 0.00320543 DNMT1_MTOR_POLA1 −0.27582 −0.71279 −0.45694 −0.78924 −0.58237 −1.11793 −1.15457 0.000335209 0.192198795 IKBKB_POLA1_TGFB1 −0.35773 −0.45694 −0.29065 −0.78623 −0.35915 −0.80145 −0.91913 0.060527203 0.202249012 MTOR_FGF2_PIK3C3 −0.71279 −0.05524 −0.52951 −0.82289 −1.25268 −0.58806 −1.1122 0.356614845 2.25719E−05 MTOR_FGF2_TGFB1 −0.71279 −0.05524 −0.29065 −0.82289 −0.91103 −0.24625 −0.8722 0.939906932 0.000310958 EGFR_ERBB2_MAP2K1 −0.26302 −0.30289 −0.09528 −0.54353 −0.26597 −0.31148 −0.3974 0.812449357 0.951805466 CDK4_EGFR_MTOR −0.24531 −0.26302 −0.71279 −0.22505 −0.89932 −0.82607 −0.92067 0.012787733 0.012970975 MAP2K

_TYMS_TGFB1 −0.09528 −0.56899 −0.29065 −0.71457 −0.28856 −0.56791 −0.7

241 1.4

138E−05 0.559346909 HDAC1_TYMS_TGFB1 −0.43459 −0.56899 −0.29065 −0.74076 −0.25654 −0.56791 −0.78811 0.089359157 0.513105385 DNMT1_FGF2_PIK3C3 −0.27582 −0.05524 −0.52951 −0.33702 −0.52531 −0.58806 −0.62205 0.052322008 0.000137979 POLA1_TYMS_

G

2 −0.45694 −0.56899 −0.05524 −0.99179 −0.69009 −0.61126 −1.01387 0.010352479 0.056990059 DNMT1_IKBKB_TYMS −0.27582 −0.35773 −0.56899 −0.39718 −0.69239 −0.59343 −0.80412 0.000499129 0.004150407 DNMT1_POLA1_TYMS −0.27582 −0.45694 −0.56899 −0.58237 −0.69239 −0.99179 −1.02112 0.000986753 0.027880379 HDAC1_IKBKB_FGF2 −0.43459 −0.35773 −0.05524 −0.43998 −0.31779 −0.27441 −0.46194 0.999902132 0.887840964 EGFR_MAP2K1_TGFB1 −0.26302 −0.09528 −0.29065 −0.26597 −0.23667 −0.28856 −0.30936 0.999154736 0.450874188 EGFR_IKBKB_FGF2 −0.26302 −0.35773 −0.05524 −0.37936 −0.30212 −0.27441 −0.41214 0.641511467 0.994754516 ERBB2_HDAC1_FGF2 −0.30289 −0.43459 −0.05524 −0.41417 −0.3165 −0.31779 −0.50264 0.354389468 0.986236631 ERBB2_FGF2_TGFB1 −0.30289 −0.05524 −0.29065 −0.3165 −0.26734 −0.24625 −0.35864 0.996633769 0.086130471 MAP2K1_PIK3C3_TGFB1 −0.09528 −0.52951 −0.29065 −0.54595 −0.28856 −0.43419 −0.58762 0.021836316 0.999037103 DNMT1_MAP2K1_TUBA1A −0.27582 −0.09528 −0.25322 −0.49617 −0.59024 −0.39044 −0.50023 0.411834782 0.024934408 EG

R_POLA1_TGFB1 −0.26302 −0.45694 −0.29065 −0.

208 −0.23

67 −0.80145 −0.81

88 0.012686553 0.228028572 MAP2K1_MTOR_FGF2 −0.09528 −0.71279 −0.05524 −0.82537 −0.31266 −0.82289 −0.77259 0.002978336 0.999521555 HDAC1_MAP2K1_FGF2 −0.43459 −0.09528 −0.05524 −0.36008 −0.31779 −0.31266 −0.49113 0.997628982 0.024723978 EGFR_HDAC1_

G

B1 −0.26302 −0.43459 −0.29065 −0.45467 −0.23667 −0.25654 −0.48824 0.422444513 0.998407833 CDK4_ERBB2_TUBA1A −0.24531 −0.30289 −0.25322 −0.40617 −0.40998 −0.55315 −0.54056 0.264479322 0.441270876 POLA1_

YMS_TGFB1 −0.45694 −0.56899 −0.29065 −0.99179 −0.80145 −0.56791 −1.1102 0.007554767 0.035241043 HDAC1_MAP2K1_POLA1 −0.43459 −0.09528 −0.45694 −0.36008 −0.98968 −0.6668 −0.84059 0.074970978 9.48678E−05 MAP2K1_FGF2_PIK3C3 −0.09528 −0.05524 −0.52951 −0.31266 −0.54595 −0.58806 −0.58093 0.008322959 0.002366436 HDAC1_TUBA1A_TGFB1 0.43459 0.25322 0.29065 0.48481 0.25654 0.43878 0.61036 0.762271014 0.121310724 IKBKB_MAP2K1_TGFB1 −0.35773 −0.09528 −0.29065 −0.25507 −0.35915 −0.28856 −0.37841 0.999992887 0.207362787 EGFR_ERBB2_MTOR −0.26302 −0.30289 −0.71279 −0.54353 −0.82607 −0.96817 −0.98714 0.00146049 0.002608133 CDK4_ERBB2_MAP2K1 −0.24531 −0.30289 −0.09528 −0.40617 −0.07834 −0.31148 −0.28492 0.999443548 0.999992874 DNMT1_EGFR_TGF

1 −0.27582 −0.26302 −0.29065 −0.47204 −0.34998 −0.23667 −0.49042 0.562844601 0.50242617

CDK4_IKBKB_TYMS −0.24531 −0.35773 −0.56899 −0.3719 −0.59996 −0.59343 −0.68444 0.002044676 0.028021473 ERBB2_POLA1_

YMS −0.30289 −0.45694 −0.56899 −0.67235 −0.44854 −0.99179 −1.02135 0.000411502 0.013572604 DNMT1_POLA1_TGFB1 −0.27582 −0.45694 −0.29065 −0.58237 −0.34998 −0.80145 −0.80358 0.029457799 0.292371516 ERBB2_POLA1_PIK3C3 −0.30289 −0.45694 −0.52951 −0.67235 −0.50956 −0.7048 −0.9281 0.003176552 0.0

0807627 DNMT1_HDAC1_FGF2 −0.27582 −0.43459 −0.05524 −0.45571 −0.33702 −0.31779 −0.49676 0.278169268 0.992156398 ERBB2_IKBKB_TYMS −0.30289 −0.35773 −0.56899 −0.25115 −0.44854 −0.59343 −0.62065 0.054023278 0.15597108 HDAC1_MTOR_FGF2 −0.43459 −0.71279 −0.05524 −1.00956 −0.

1779 −0.82289 −0.98004 0.028877076 0.607421086 DNMT1_EGFR_MTOR −0.27582 −0.26302 −0.71279 −0.47204 −0.78924 −0.82607 −0.90712 0.00471385 0.003716456 DNMT1_PIK3C3_TGFB1 −0.27582 −0.52951 −0.29065 −0.52531 −0.34998 −0.43419 −0.60163 0.14677148 0.99458076 DNMT1_IKBKB_PIK3C3 −0.27582 −0.35773 −0.52951 −0.39718 −0.52531 −0.33448 −0.64872 0.026177035 0.122002027 CDK4_TYMS_TGFB1 −0.24531 −0.56899 −0.29065 −0.59996 −0.21676 −0.56791 −0.61261 0.05939964 0.999524515 DNMT1_IKBKB_MTOR −0.27582 −0.35773 −0.71279 −0.39718 −0.78924 −0.77193 −0.86826 0.004014228 0.016328564 CDK4_TUBA1A_IGFB1 −0.24531 −0.25322 −0.29065 −0.40998 −0.21676 −0.43878 −0.42084 0.76574014 0.77904592 MTOR_

UBA1A_FGF2 −0.71279 −0.25322 −0.05524 −1.01377 −0.82289 −0.69614 −1.12834 0.213482153 0.000121962 EGFR_MAP2K1_FGF2 −0.26302 −0.09528 −0.05524 −0.26597 −0.30212 −0.31266 −0.29491 0.999847683 0.444539803 MAP2K1_MTOR_TGFB1 −0.09528 −0.71279 −0.29065 −0.82537 −0.28856 −0.91103 −0.83414 0.001133882 0.975315715 ERBB2_IKBKB_POLA1 −0.30289 −0.35773 −0.45694 −0.25115 −0.67235 −0.78623 −0.80626 0.011958319 0.032475952 CDK4_MAP2K1_FGF2 −0.24531 −0.09528 −0.05524 −0.07834 −0.15718 −0.31266 −0.27451 0.999843732 0.419869513 EGFR_HDAC1_IKBKB −0.26302 −0.43459 −0.35773 −0.45467 −0.37936 −0.43998 −0.53034 0.084447366 0.914960916 IKBKB_

YMS_FGF2 −0.35773 −0.56899 −0.05524 −0.59343 −0.27441 −0.61126 −0.6848 0.047011372 0.894596612 CDK4_MTOR_FGF2 −0.24531 −0.71279 −0.05524 −0.89932 −0.15718 −0.82289 −0.78241 0.037361267 0.999070094 DNMT1_IKBKB_TGFB1 −0.27582 −0.35773 −0.29065 −0.39718 −0.34998 −0.35915 −0.42156 0.817897885 0.995659025 IKBKB_MAP2K1_TUBA1A −0.35773 −0.09528 −0.25322 −0.25507 −0.49372 −0.39044 −0.45977 0.938852415 0.039864306 DNMT1_IKBKB_TUBA1A −0.27582 −0.35773 −0.25322 −0.39718 −0.59024 −0.49372 −0.65919 0.015691936 0.083299124 DNMT1_MTOR_PIK3C3 −0.27582 −0.71279 −0.52951 −0.78924 −0.52531 −1.25268 −1.23944 7.00877E−06 0.050492978 EGFR_MAP2K1_PIK3C3 −0.26302 −0.09528 −0.52951 −0.26597 −0.562

1 −0.54595 −0.5178 0.347332467 0.027110974 DNMT1_MTOR_

G

1 −0.27582 −0.71279 −0.29065 −0.78924 −0.34998 −0.91103 −0.89211 0.008391419 0.885453653 CDK4_IKBKB_POLA1 −0.24531 −0.35773 −0.45694 −0.3719 −0.6393 −0.78623 −0.73515 0.016264562 0.081633961 CDK4_M

OR_POLA1 −0.24531 −0.71279 −0.45694 −0.89932 −0.6393 −1.11793 −1.06681 0.002384557 0.429559835 DNMT1_TUBA1A_TYMS −0.27582 −0.25322 −0.56899 −0.59024 −0.69239 −0.86356 −0.86163 0.000448336 0.0002

0797 ERBB2_TYMS_PIK3C3 −0.30289 −0.56899 −0.52951 −0.44854 −0.50956 −0.63063 −0.78056 0.001933195 0.445735259 CDK4_TYMS_FGF2 −0.24531 −0.56899 −0.05524 −0.59996 −0.15718 −0.61126 −0.55814 0.135123598 0.999999866 CDK4_EGFR_HDAC1 −0.24531 −0.26302 −0.4345

−0.22505 −0.37

49 −0.45467 −0.40054 0.819753003 0.870958631 CDK4

DNM

1_TUBA1A −0.24531 −0.27582 −0.25322 −0.29118 −0.40998 −0.59024 −0.53014 0.197971029 0.271938252 EGFR_TUBA1A_FGF2 −0.26302 −0.25322 −0.05524 −0.60402 −0.30212 −0.69614 −0.65348 0.079108506 0.067957296 EGFR_ERBB2_HDAC1 −0.26302 −0.30289 −0.43459 −0.54353 −0.45467 −0.41417 −0.67102 0.007700803 0.01823622 EGFR_HDAC1_PIK3C3 −0.26302 −0.43459 −0.52951 −0.45467 −0.56261 −0.6072

−0.69004 0.014143671 0.28904632 DNMT1_HDAC1_MTOR −0.27582 −0.43459 −0.71279 −0.45571 −0.78924 −1.00956 −0.97801 0.000347588 0.009694624 DNMT1_EGFR_MAP2K1 −0.27582 −0.26302 −0.09528 −0.47204 −0.49617 −0.26597 −0.44472 0.6398

7523 0.56721908 CDK4_POLA1_PIK3C3 −0.24531 −0.45694 −0.52951 −0.6393 −0.44216 −0.7048 −0.85432 0.005915217 0.141927011 IKBKB_MAP2K1_FGF2 −0.35773 −0.

9528 −0.05524 −0.25507 −0.27441 −0.312

6 −0.35577 1 0.095903324 MAP2K1_TUBA1A_PIK3C3 −0.09528 −0.25322 −0.52951 −0.39044 −0.54595 −0.949 −0.72584 0.018187264 0.119384958 FGF2_PIK3C3_TGFB1 −0.05524 −0.52951 −0.29065 −0.58806 −0.24625 −0.43419 −0.55935 0.00642399 0.999970384 IKBKB_

YMS_TGFB1 −0.35773 −0.56899 −0.29065 −0.59343 −0.35915 −0.56791 −0.60839 0.274048858 0.999715519 ERBB2_TUBA1A_TYMS −0.30289 −0.25322 −0.56899 −0.55315 −0.44854 −0.86356 −0.84605 0.004309034 0.001692166 CDK4_MTOR_

G

B1 −0.

4531 −0.71279 −0.29065 −0.89932 −0.21676 −0.91103 −0.86877 0.076776536 0.976533714 ERBB2_HDAC1_PIK3C3 −0.30289 −0.43459 −0.52951 −0.41417 −0.50956 −0.60726 −0.62159 0.054144269 0.502663356 CDK4_DNMT1_PIK3C3 −0.24531 −0.27582 −0.52951 −0.29118 −0.44216 −0.52531 −0.49804 0.263644678 0.361222376 DNMT1_HDAC1_TGFB1 −0.27582 −0.43459 −0.29065 −0.45571 −0.34998 −0.25654 −0.46099 0.633925498 0.999975285 ERBB2_MAP2K1_PIK3C3 −0.30289 −0.09528 −0.52951 −0.31148 −0.50956 −0.54595 −0.52193 0.447628521 0.018095289 DNMT1_ERBB2_TGFB1 −0.27582 −0.30289 −0.29065 −0.5251 −0.34998 −0.26734 −0.48722 0.513435608 0.638637125 EGFR_ERBB2_PIK3C3 −0.26302 −0.30289 −0.52951 −0.54353 −0.56261 −0.50956 −0.74419 0.002244872 0.005379722 CDK4_TUBA1A_FGF2 −0.24531 −0.25322 −0.05524 −0.40998 −0.15718 −0.69614 −0.61127 0.098279686 0.094633994 HDAC1_TYMS_FGF2 −0.43459 −0.56899 −0.05524 −0.74076 −0.31779 −0.61126 −0.71552 0.182847171 0.801318389 ERBB2_TUBA1A_TGFB1 −0.30289 −0.25322 −0.29065 −0.55315 −0.26734 −0.43878 −0.51344 0.583174122 0.375934567 POLA1_TUBA1A_PIK3C3 −0.45694 −0.25322 −0.52951 −0.83211 −0.7048 −0.949 −1.07202 0.085623076 0.007535546 ERBB2_HDAC1_TGFB1 −0.30289 −0.43459 −0.29065 −0.41417 −0.26734 −0.25654 −0.36562 0.995732328 0.9934137 ERBB2_IKBKB_MTOR −0.30289 −0.35773 −0.71279 −0.25115 −0.96817 −0.77193 −0.98515 0.000597249 0.001973539 MAP2K1_MTOR_TUBA1A −0.09528 −0.71279 −0.25322 −0.82537 −0.39044 −1.01377 −0.76722 0.002766811 0.999655369 DNMT1_ERBB2_IKBKB −0.27582 −0.30289 −0.35773 −0.5251 −0.39718 −0.25115 −0.54061 0.177187338 0.257302231 DNMT1_ERBB2_PIK3C3 −0.27582 −0.30289 −0.52951 −0.5251 −0.52531 −0.50956 −0.71015 0.004709921 0.008159256 DNMT1_HDAC1_POLA1 −0.27582 −0.43459 −0.45694 −0.45571 −0.58237 −0.98968 −0.9205 0.001801948 0.032746056 ERBB2_MTOR_TYMS −0.30289 −0.71279 −0.56899 −0.96817 −0.44854 −1.0865 −1.19109 3.10385E−05 0.087158228 ERBB2_IKBKB_PIK3C3 −0.30289 −0.35773 −0.52951 −0.25115 −0.50956 −0.33448 −0.52119 0.269208763 0.569984167 HDAC1_POLA1_FGF2 −0.43459 −0.45694 −0.05524 −0.98968 −0.31779 −0.69009 −0.77732 0.120922573 0.188779077 HDAC1_PIK3C3_TGFB1 −0.43459 −0.52951 −0.29065 −0.60726 −0.25654 −0.43419 0.54929 0.9402271 0.999995913 HDAC1_IKBKB_TUBA1A −0.43459 −0.35773 −0.25322 −0.43998 −0.48481 −0.49372 −0.57886 0.832374505 0.438715038 CDK4_DNMT1_EGFR −0.24531 −0.27582 −0.26302 −0.29118 −0.22505 −0.47204 −0.36715 0.88256087 0.961024022 DNMT1_MAP2K1_TYMS −0.27582 −0.09528 −0.56899 −0.49617 −0.69239 −0.71457 −0.71444 0.006095908 3.854E−05 CDK4_DNMT1_POLA1 −0.24531 −0.27582 −0.45694 −0.29118 −0.6393 −0.58237 −0.56423 0.261701465 0.33153578 CDK4_IKBKB_TUBA1A −0.24531 −0.35773 −0.25322 −0.3719 −0.40998 −0.49372 −0.41409 0.701546821 0.997276005 IKBKB_TOP1_PIK3C3 −0.35773 −1.04454 −0.52951 −0.77903 −0.33448 −0.91968 −1.0245 0.000701332 0.999998826 CDK4_DNMT1_ERBB2 −0.24531 −0.27582 −0.30289 −0.29118 −0.40617 −0.5251 −0.41553 0.615886485 0.763310307 CDK4_HDAC1_IKBKB −0.24531 −0.43459 −0.35773 −0.37949 −0.3719 −0.43998 −0.45132 0.485462568 0.999997572 ERBB2_TOP1_TYMS −0.30289 −1.04454 −0.56899 −0.74886 −0.44854 −1.09903 −1.13705 3.98718E−05 0.992936194 TYMS_FGF2_TGFB1 −0.56899 −0.05524 −0.29065 −0.61126 −0.56791 −0.24625 −0.54518 0.999989503 0.00513216 MAP2K1_FGF2_TGFB1 −0.09528 −0.05524 −0.29065 −0.31266 −0.28856 −0.24625 −0.24468 0.76910791 0.524527976 IKBKB_POLA1_FGF2 −0.35773 −0.45694 −0.05524 −0.78623 −0.27441 −0.69009 −0.6878 0.141115451 0.525218028 IKBKB_MAP2K1_TYMS −0.35773 −0.09528 −0.56899 −0.25507 −0.59343 −0.71457 −0.71211 0.013043281 2.36184E−06 ERBB2_FGF2_PIK3C3 −0.30289 −0.05524 −0.52951 −0.3165 −0.50956 −0.58806 −0.52861 0.323245701 0.001459051 IKBKB_TUBA1A_TGFB1 −0.35773 −0.25322 −0.29065 −0.49372 −0.35915 −0.43878 −0.43398 0.993569398 0.740884156 CDK4_TOP1_TUBA1A −0.24531 −1.04454 −0.25322 −0.88189 −0.40998 −1.10077 −1.09048 0.000620446 0.999925587 CDK4_MAP2K1_TYMS −0.24531 −0.09528 −0.56899 −0.07834 −0.59996 −0.71457 −0.59575 0.028516648 0.000363573 CDK4_EGFR_IKBKB −0.24531 −0.26302 −0.35773 −0.22505 −0.3719 −0.37936 −0.26979 0.999963935 0.99999998 CDK4_EGFR_TUBA1A −0.24531 −0.26302 −0.25322 −0.22505 −0.40998 −0.60402 −0.4826 0.53635809 0.58598728 DNMT1_EGFR_TYMS −0.27582 −0.26302 −0.56899 −0.47204 −0.69239 −0.83951 −0.74779 0.004758987 0.003459964 DNMT1_HDAC1_TYMS −0.27582 −0.43459 −0.56899 −0.45571 −0.69239 −0.74076 −0.75667 0.002261139 0.081442936 ERBB2_MAP2K1_MTOR −0.30289 −0.09528 −0.71279 −0.31148 −0.96817 −0.82537 −0.75665 0.081044919 0.004240715 CDK4_POLA1_FGF2 −0.24531 −0.45694 −0.05524 −0.6393 −0.15718 −0.69009 −0.5614 0.205127474 0.971213376 EGFR_MTOR_POLA1 −0.26302 −0.71279 −0.45694 −0.82607 −0.6208 −1.11793 −1.00515 0.010571264 0.651515631 DNMT1_TUBA1A_TGFB1 −0.27582 −0.25322 −0.29065 −0.59024 −0.34998 −0.43878 −0.50506 0.444645458 0.347292547 CDK4_ERBB2_IKBKB −0.24531 −0.30289 −0.35773 −0.40617 −0.3719 −0.25115 −0.38649 0.762172229 0.965124709 EGFR_POLA1_TYMS −0.26302 −0.45694 −0.56899 −0.6208 −0.83951 −0.99179 −0.91769 0.001217547 0.051725087 EGFR_HDAC1_POLA1 −0.26302 −0.43459 −0.45694 −0.45467 −0.6208 −0.98968 −0.87254 0.001561968 0.041679564 ERBB2_POLA1_TUBA1A −0.30289 −0.45694 −0.25322 −0.67235 −0.55315 −0.83211 −0.75271 0.044690777 0.358788498 EGFR_IKBKB_PIK3C3 −0.26302 −0.35773 −0.52951 −0.37936 −0.56261 −0.33448 −0.53782 0.169861142 0.571928002 HDAC1_TUBA1A_FGF2 −0.43459 −0.25322 −0.05524 −0.48481 −0.31779 −0.69614 −0.7476 0.389915349 0.049978671 EGFR_TUBA1A_TYMS −0.26302 −0.25322 −0.56899 −0.60402 −0.83951 −0.86356 −0.7855 0.006027287 0.004881863 TUBA1A_FGF2_PIK3C3 −0.25322 −0.05524 −0.52951 −0.69614 −0.949 −0.58806 −0.83669 0.041107124 0.001967045 MAP2K1_POLA1_TGFB1 −0.09528 −0.45694 −0.29065 −0.6668 −0.28856 −0.80145 −0.56764 0.039255191 0.971867206 IKBKB_TYMS_PIK3C3 −0.35773 −0.56899 −0.52951 −0.59343 −0.33448 −0.63063 −0.73112 0.015189271 0.658032905 CDK4_ERBB2_TYMS −0.24531 −0.30289 −0.56899 −0.40617 −0.59996 −0.44854 −0.58325 0.081724282 0.171103548 EGFR_TOP1_MAP2K1 −0.26302 −1.04454 −0.09528 −0.89535 −0.26597 −0.87661 −0.91799 0.003320643 0.967730884 CDK4_POLA1_TUBA1A −0.24531 −0.45694 −0.25322 −0.6393 −0.40998 −0.83211 −0.68424 0.070705121 0.637137258 MAP2K1_POLA1_TYMS −0.09528 −0.45694 −0.56899 −0.6668 −0.71457 −0.99179 −0.84072 5.19977E−05 0.10406536 DNMT1_TOP1_TUBA1A −0.27582 −1.04454 −0.25322 −0.92996 −0.59024 −1.10077 −1.23864 2.39718E−06 0.810673214 DNMT1_EGFR_IKBKB −0.27582 −0.26302 −0.35773 −0.47204 −0.39718 −0.37936 −0.43341 0.743060731 0.675884686 EGFR_ERBB2_TGFB1 −0.26302 −0.30289 −0.29065 −0.54353 −0.23667 −0.26734 −0.43775 0.677474537 0.855222857 HDAC1_IKBKB_TGFB1 −0.43459 −0.35773 −0.29065 −0.43998 −0.25654 −0.35915 −0.39634 0.999744812 0.999708572 CDK4_TUBA1A_TYMS −0.24531 −0.25322 −0.56899 −0.40998 −0.59996 −0.86356 −0.71144 0.01597268 0.014381971 MTOR_TUBA1A_PIK3C3 −0.71279 −0.25322 −0.52951 −1.01377 −1.25268 −0.949 −1.26418 0.222546491 0.001606358 EGFR_ERBB2_TYMS −0.26302 −0.30289 −0.56899 −0.54353 −0.83951 −0.44854 −0.74267 0.003634537 0.008219641 CDK4_FGF2_PIK3C3 −0.24531 −0.05524 −0.52951 −0.15718 −0.44216 −0.58806 −0.43273 0.702820779 0.054955501 DNMT1_ERBB2_TYMS −0.27582 −0.30289 −0.56899 −0.5251 −0.69239 −0.44854 −0.69231 0.018670403 0.029211576 DNMT1_IKBKB_MAP2K1 −0.27582 −0.35773 −0.09528 −0.39718 −0.49617 −0.25507 −0.44922 0.566279426 0.952167024 ERBB2_MTOR_PIK3C3 −0.30289 −0.71279 −0.52951 −0.96817 −0.50956 −1.25268 −1.1505 9.55438E−05 0.1513477 CDK4_HDAC1_TUBA1A −0.24531 −0.43459 −0.25322 −0.37949 −0.40998 −0.48481 −0.43934 0.763798155 1 IKBKB_MTOR_FGF2 −0.35773 −0.71279 −0.05524 −0.77193 −0.27441 −0.82289 −0.77322 0.073620074 0.99916648 IKBKB_MTOR_TYMS −0.35773 −0.71279 −0.56899 −0.77193 −0.59343 −1.0865 −1.03621 0.00039978 0.278826248 TYMS_PIK3C3_TGFB1 −0.56899 −0.52951 −0.29065 −0.63063 −0.56791 −0.43419 −0.68918 0.932670788 0.779394165 CDK4_MAP2K1_PIK3C3 −0.24531 −0.09528 −0.52951 −0.07834 −0.44216 −0.54595 −0.38172 0.849696703 0.166238548 ERBB2_MTOR_TGFB1 −0.30289 −0.71279 −0.29065 −0.96817 −0.26734 −0.91103 −0.8484 0.023777621 0.955774262 POLA1_PIK3C3_TGFB1 −0.45694 −0.52951 −0.29065 −0.7048 −0.80145 −0.43419 −0.91803 0.136474049 0.237863874 CDK4_ERBB2_HDAC1 −0.24531 −0.30289 −0.43459 −0.40617 −0.37949 −0.41417 −0.42738 0.698439218 0.907831432 HDAC1_MAP2K1_PIK3C3 −0.43459 −0.09528 −0.52951 −0.36008 −0.60726 −0.54595 −0.56648 0.90701791 0.012496068 EGFR_MTO

_TUBA1A −0.26302 −0.71279 −0.25322 −0.82607 −0.60402 −1.01377 −0.89957 0.010943874 0.8

5317221 TYMS_PIK3C3_FGF2 −0.56899 0.52951 −0.05524 −0.63063 0.61126 −0.58806 −0.73979 0.728963962 0.503344933 EGFR

IKBKB

TYMS −0.26302 −0.35773 −0.56899 −0.37936 −0.83951 −0.59343 −0.77871 0.000268569 0.003993143 CDK4_TOP1_FGF2 −0.24531 −1.04454 −0.05524 −0.88189 −0.15718 −0.81541 −0.78087 0.014583903 0.497242395 ERBB2_IKBKB_TOP1 −0.30289 −0.35773 −1.04454 −0.25115 −0.74886 −0.77903 −0.8739 0.00

06405 0.009477197 ERBB2_IKBKB_TGF

1 −0.30289 −0.35773 −0.29065 −0.25115 −0.26734 −0.35915 −0.2392

0.994892292 0.900718132 CDK4_TOP1_TGFB1 −0.24531 −1.04454 −0.29065 −0.88189 −0.21676 −1.01887 −0.84136 0.008859094 0.772616512 MAP2K1_TOP1_TGFB1 −0.39528 −1.04454 −0.29065 −0.87661 −0.28856 −1.01887 −0.90947 0.004024019 0.985749339 MAP2K1_TOP1_FGF2 −0.09528 −1.04454 −0.05524 −0.87661 −0.31266 −0.81541 −0.93345 0.001200671 0.993522768 DNMT1_ERBB2_MAP2K1 −0.27582 −0.30289 −0.09528 −0.5251 −0.49617 −0.31148 −0.37455 0.955972034 0.990123335 IKBKB_

BA1A_TYMS −0.35773 −0.

5322 −3.56899 −0.4937

−0.59343 −0.86356 −0.79541 0.003553734 0.000187511 DNMT1_HDAC1_

BA1A −0.27582 −0.43459 −0.25322 −0.45571 −0.59024 −0.48481 −0.59774 0.065807347 0.653160238 ERBB2_TUBA1A_FGF2 −0.30289 −0.25322 −0.05524 −0.55315 −0.3165 −0.69614 −0.57034 0.315186362 0.175507708 ERBB2_MTOR_

BA1A −0.30289 −0.71279 −0.25322 −0.96817 −0.55315 −1.01377 −0.88537 0.015610598 0.908074586 EGFR_

BA1A_

G

1 −0.26302 −0.25322 −0.29065 −0.60402 −0.23667 −0.43878 −0.46231 0.736984533 0.696746871 CDK4_ERBB2_PIK3C3 −0.24531 −0.30289 −0.52951 −0.40617 −0.44216 −0.50956 −0.50255 0.243337358 0.455763603 CDK4_HDAC1_TYMS −0.24531 −0.43459 −3.56899 −0.37949 −0.59996 −0.74076 −0.60064 0.07964713 0.727056779 MAP2K1_M

OR_PIK3C3 −0.09528 −0.71279 −0.52951 −0.82537 −0.54595 −1.25268 −0.91748 0.001220404 0.872510392 ERBB2_HDAC1_TUBA1A −0.30289 −0.43459 −0.25322 −0.41417 −0.55315 −0.48481 −0.5467 0.319588231 0.93175061 EGFR_MTOR_PIK3C3 −0.26302 −0.71279 −0.52951 −0.82607 −0.56261 −1.25268 −1.07335 0.000

51599 0.376443571 DNMT1_HDAC

_

OP1 −0.27582 −0.43459 −1.04454 −0.45571 −0.92996 −0.81956 −1.05567 1.56697E−05 0.000980845

RBB2_MAP2K1_TYMS −0.30289 −0.09528 −0.56899 −0.31148 −0.44854 −0.71457 −0.57143 0.153

75878 0.001580122 M

OR_POLA1_TUBA1A −0.71279 −0.45604 −0.25322 −1.117

3 −1.01377 −0.83211 −1.09486 0.331355836 0.023

70225 TUBA1A

FGF2

TGFB1 −0.25322 −0.05524 −0.29065 −0.69614 −0.43878 −0.24625 −0.53564 0.333459311 0.016124162 CDK4_EGFR_PIK3C3 −0.24531 −0.26302 −0.52951 −0.22505 −0.44216 −0.56261 −0.35488 0.94193699 0.970235853 HDAC1_TOP1_

G

2 −0.43459 −1.04454 −0.05524 −0.819

6 −0.31779 −0.81541 −0.90824 0.02064195 0.928782583

GFR_PIK3C3_TG

B1 −0.26302 −0.52951 −0.29065 −0.56261 −0.23667 −0.43419 −0.39784 0.91299

176 0.916365812

GFR_M

OR_TYMS −0.26302 −0.71279 −0.56899 −0.82607 −0.83951 −1.0865 −1.0948 0.000146874 0.251977691 POLA1_

YMS_PIK3C3 −0.45694 −0.56899 −0.52951 −0.99179 −0.7048 −0.63063 −1.06375 0.011505501 0.053502746 IKBKB_MTOR_TGFB1 −0.35773 −0.71279 −0.29065 −0.77193 −0.35915 −0.91103 −0.81074 0.071729031 0.992363179

UBA1A_

YMS_FGF2 −0.25322 −0.56899 −0.05524 −0.86356 −0.69614 −0.61126 −0.80676 0.006829303 0.570532836 EGFR_E

BB2_IKBKB −0.26302 −0.30289 −0.35773 −0.54353 −0.37936 −0.25115 −0.44212 0.508800726 0.737103119 EGFR_MAP2K1_TYMS −0.26302 −0.09528 −0.56899 −0.26597 −0.83951 −0.71457 −0.51771 0.18711904 0.005417724 IKBKB_MTOR_POLA1 −0.35773 −0.71279 −0.45694 −0.77193 −0.78623 −1.11793 −1.03901 0.005780127 0.442450563 IKBKB_MAP2K1_POLA1 −0.35773 −0.09528 −0.45694 −0.25507 −0.78623 −0.6668 −0.56448 0.582694294 0.016010126 HDAC1_MAP2K1_TOP1 −0.43459 −0.09528 −1.04454 −0.3

008 −0.81956 −0.87661 −0.9425 0.033888127 5.8056E−05 HDAC1_TUBA1A_TYMS −0.43459 −0.25322 −0.56899 −0.48481 −0.74076 −0.86356 −0.83593 0.032223149 0.000489096 EGFR_TOP1_FGF2 −0.26302 −1.04454 −0.05524 −0.89535 −0.30212 −0.81541 −0.88429 0.003115096 0.899048153 C

K4_DNMT1_MAP2K1 −0.24531 −0.27582 −0.09528 −0.29118 −0.07834 −0.4961

−0.27851 0.999766652 1 MAP2K1_TYMS_PIK3C3 −0.

9528 −0.56899 −0.52951 −0.71457 −0.54595 −0.63063 −0.78014 1.83452E−05 0.512325554 C

K4_MTOR_HDAC1 −0.24531 −0.71279 −0.43459 −0.89932 −0.37949 −1.00956 −0.86944 0.021273127 0.952123379 IKBKB_MAP2K1_PIK3C3 −0.35773 −0.09528 −0.52951 −0.25507 −0.33448 −0.54595 −0.43414 0.990489565 0.101484954 CDK4_DNMT1_TYMS −0.24531 −0.27582 −0.56899 −0.29118 −0.59996 −0.69239 −0.46778 0.356097197 0.480452137 DNMT1_EGFR_PIK3C3 −0.27582 −0.26302 0.52951 0.47204 0.52531 0.56261 0.5304 0.279732974 0.234090126 DNMT1

MAP2K1_PIK3C3 −0.27582 −0.09528 −0.52951 −0.49617 −0.52531 −0.54595 −0.55255 0.240532933 0.010566304 HDAC1_FGF2_PIK3C3 −0.43459 −0.05524 −0.52951 −0.31779 −0.60726 −0.58806 −0.54949 0.938655512 0.003702547 DNMT1_ERBB2_HDAC1 −0.27582 −0.30289 −0.43459 −0.5251 −0.45571 −0.41417 −0.48647 0.389792965 0.520237367 HDAC1_MTOR_TGFB1 −0.43459 −0.71279 −0.29065 −1.00956 −0.25654 −0.91103 −0.87227 0.132345361 0.933650256 MTOR_POLA1_PIK3C3 −0.71279 −0.45694 −0.52951 −1.11793 −1.25268 −0.7048 −1.23538 0.176786196 0.01176398

OP1_FGF2_

GHB1 −1.04454 −0.05524 −0.29065 −0.81541 −1.01887 −0.24625 −0.81603 0.681434549 0.000225282 CDK4_IKBKB_TGFB1 −0.24531 −0.35773 −0.29065 −0.3719 −0.21676 −0.35915 −0.18294 0.99503723 0.570461318 EGFR_HDAC1_MTOR −0.26302 −0.43459 −0.71279 −0.45467 −0.82607 −1.00956 −0.79157 0.022326416 0.216386667 CDK4_TOP1_TYMS −0.24531 −1.04454 −0.56899 −0.88189 −0.59996 −1.09903 −1.16343 1.69784E−06 0.968102529 CDK4_EGFR_TOP1 −0.24531 −0.26302 −1.04454 −0.22505 −0.88189 −0.89535 −0.78

38 0.015057996 0.01582074 HDAC1_IKBKB_PIK3C3 −0.43459 −0.35773 −0.52951 −0.43998 −0.60726 −0.33448 −0.48401 0.997622466 0.799126743 IKBKB_FGF2_PIK3C3 −0.35773 −0.05524 −0.52951 −0.27441 −0.33448 −0.58806 −0.45999 0.932779706 0.007938251 CDK4_IKBKB_PIK3C3 −0.24531 −0.35773 −0.52951 −0.3719 −0.44216 −0.33448 −0.41357 0.602916334 0.995387995 IKBKB_PIK3C3_TGFB1 −0.35773 −0.52951 −0.29065 −0.33448 −0.35915 −0.43419 −0.40051 0.999497393 0.871093468 DNMT1_EGFR_HDAC1 −0.27582 −0.26302 −0.43459 −0.47204 −0.45571 −0.45467 −0.41082 0.808085758 0.74193146 ERBB2_TOP1_TGFB1 −0.30289 −1.04454 −0.29065 −0.74886 −0.26734 −1.01887 −0.82556 0.010665585 0.66090131 CDK4_MTOR_TYMS −0.24531 −0.71279 −0.56899 −0.89932 −0.59996 −1.0865 −0.97117 0.002240866 0.61758867 CDK4_TUBA1A_PIK3C3 −0.24531 −0.25322 −0.52951 −0.40998 −0.44216 −0.949 −0.6971 0.178318486 0.168909968 IKBKB_MTOR_TUBA1A −0.35773 −0.71279 −0.25322 −0.77193 −0.49372 −1.01377 −0.87063 0.015815572 0.896741119 HDAC1_IKBKB_MTOR −0.43459 −0.35773 −0.

1279 −0.43998 −1.00956 −0.77193 −0.86631 0.097423879 0.030583253 HDAC1_POLA1_TYMS 0.43459 −0.45694 −0.56899 −0.98968 −0.74076 −0.99179 −1.05587 0.004010482 0.008127223 CDK4_

OP1_MAP2K1 −0.24531 −1.04454 −0.09528 −0.88189 −0.07834 −0.87661 −0.61959 0.162475164 0.085037372 DNMT1_TUBA1A_PIK3C3 −0.27582 −0.25322 −0.52951 −0.59024 −0.52531 −0.949 −0.71957 0.130672

34 0.100716136 IKBKB_MAP2K1_TOP1 0.35773 0.09528 −1.04454 0.25507 0.77903 0.87661 0.78875 0.063082719 0.000634163

UBA1A_TYMS_TGFB1 −0.25322 −0.56899 −0.29065 −0.86356 −0.43878 −0.56791 −0.64335 0.07130711 0.994861974 ERBB2_TOP1_FGF2 −0.30289 −1.04454 −0.05524 −0.74886 −0.3165 −0.81541 −0.84802 0.004676349 0.716802474 ERBB2_MAP2K1_TOP1 −0.30289 −0.09528 −1.04454 −0.31148 −0.74886 −0.87661 −0.84283 0.014897336 0.000356993 CDK4_PIK3C3_

GFB1 −0.24531 −0.52951 −0.29065 −0.44216 −0.21

7

−0.43419 −0.23158 0.999999642 0.17

141287 ERBB2_HDAC1_POLA1 −0.30289 −0.43459 −0.45694 −0.41417 −0.67235 −0.98968 −0.77499 0.030646689 0.208026591 DNM

1_TYMS_PIK3C3 −0.27582 −0.56899 −0.52951 −0.69239 −0.52531 −0.63063 −0.70327 0.013878123 0.870567147 CDK4_TYMS_PIK3C3 −0.24531 −0.56899 −0.52951 −0.59996 −0.44216 −0.63063 −0.60973 0.043796121 0.999565845 EGFR_TOP1_TUBA1A −0.26302 −1.04454 −0.25322 −0.89535 −0.60402 −1.10077 −1.12323 0.000216382 0.998455251 ERBB2_TUBA1A_PIK3C3 −0.30289 −0.25322 −0.52951 −0.55315 −0.50956 −0.949 −0.72605 0.163169116 0.100052175 CDK4_HDAC1_TOP1 −0.24531 −0.43459 −1.04454 −0.37949 −0.88189 −0.81956 −0.89765 0.005024707 0.072169652 MTOR_POLA1_TGFB1 −0.71279 −0.45694 −0.29065 −1.11793 −0.91103 −0.80145 −0.98759 0.717073157 0.144163109 IKBKB_TOP1_

G

2 −0.35773 −1.04454 −0.05524 −0.77903 −0.27441 −0.81541 −0.79222 0.04332238 0.505363953 CDK4_HDAC1_POLA1 −0.24531 −0.43459 −0.45694 −0.37949 −0.6393 −0.98968 −0.70766 0.118809039 0.577920751 DNMT1_TOP1_MTOR −0.27582 −1.04454 −0.71279 −0.92996 −0.78924 −0.84956 −1.30117 8.90951E−06 0.683935172 TOP1_TYMS_FGF2 −1.04454 −0.56899 −0.05524 −1.09903 −0.81541 −0.61126 −1.1225 0.996394064 0.010591336 CDK4_HDAC1_PIK3C3 −0.24531 −0.43459 −0.52951 −0.37949 −0.44216 −0.60726 −0.3736 0.911822606 0.997344896 HDAC1_TUBA1A_PIK3C3 0.43459 0.25322 0.52951 0.48481 0.60726 0.949 0.84805 0.194599243 0.020904649 ERBB2

MTOR

FGF2 −0.30289 −0.71279 −0.05524 −0.96817 −0.3165 −0.82289 −0.5899 0.437388699 0.976590726 EGFR_TYMS_TGFB1 −0.26302 −0.56899 −0.29065 −0.83951 −0.23667 −0.56791 −0.59365 0.136287014 0.99998876 CDK4_TOP1_PIK3C3 −0.24531 −1.04454 −0.52951 −0.88189 −0.44216 −0.91968 −0.94849 0.000562753 0.990148184 DNMT1_TOP1_PIK3C3 −0.27582 −1.04454 −0.52951 −0.92996 −0.52531 −0.91968 −1.03028 3.54991E−05 0.99999976

HDAC1_TYMS_PIK3C3 −0.43459 −0.56899 −0.52951 −0.74076 −0.60726 −0.63063 −0.73012 0.113619597 0.692691862 DNMT1_MTOR_TUBA1A −0.27582 −0.71279 −0.25322 −0.78924 −0.59024 −1.01377 −0.76042 0.043758213 0.999781511 EGFR_TUBA1A_PIK3C3 −0.26302 −0.25322 −0.52951 −0.60402 −0.56261 −0.949 −0.

6593 0.269068647 0.246986732 CDK4_ERBB2_TGFB1 −0.24531 −0.30289 −0.29065 −0.40617 −0.21676 −0.26734 −0.14319 0.956620542 0.715295576 TOP1_PIK3C3_TGFB1 −1.04454 −0.52951 −0.29065 −0.91968 −1.01887 −0.43419 −0.

9308 0.999718257 0.04940146 CDK4_EGFR_TYMS −0.24531 −0.26302 −0.56899 −0.22505 −0.59996 −0.83951 −0.52751 0.188759609 0.217756511 TOP1_TYMS_TGFB1 −1.04454 −0.56899 −0.29065 −1.09903 −1.01887 −0.56791 −1.05445 0.999999983 0.049710938 MAP2K1_TOP1_TUBA1A −0.09528 −1.04454 −0.25322 −0.87661 −0.39044 −1.10077 −0.87665 0.001003912 0.923027752 IKBKB_TUBA1A_FGF2 −0.35773 −0.25322 −0.05524 −0.49372 −0.27441 −0.69614 −0.18791 0.862028816 0.349794472 IKBKB_TOP1_TUBA1A −0.35773 −1.04454 −0.25322 −0.77903 −0.49372 −1.10077 −0.97218 0.005308204 0.998089398 MTOR_PIK3C3_TGFB1 −0.71279 −0.52951 −0.29065 −1.25268 −0.91103 −0.43419 −0.9742 0.731091058 0.193084706 MTOR_PO

A1_TOP1 −0.71279 −0.45694 −1.04454 −1.11793 −0.84956 −0.83822 −1.58956 0.014022856 0.000640812 CDK4_IKBKB_TOP1 0.24531 −0.35773 1.04454

.3719 0.88189 0.77903 0.84189 0.002250135 0.014067164 MTOR

YMS

FGF2 −0.71279 −0.56899 −0.05524 −1.0865 −0.82289 −0.61126 −0.8165 0.991294609 0.645789191 HDAC1_MTOR_TUBA1A −0.43459 −0.71279 −0.25322 −1.00956 −0.48481 −1.01377 −0.8726 0.108827321 0.925081039 ERBB2_HDAC1_MTOR −0.30289 −0.43459 −0.71279 −0.41417 −0.96817 −1.00956 −0.82461 0.020415295 0.143546357 MTOR_TYMS_TGFB1 −0.71279 −0.56899 −0.29065 −1.0865 −0.91103 −0.56791 −0.90168 0.865119757 0.37158938 MAP2K1_MTOR_POLA1 −0.09528 −0.71279 −0.45694 −0.82537 −0.6668 −1.11793 −0.79677 0.013161712 0.997814847 EGFR_TOP1_PIK3C3 −0.26302 −1.04454 −0.52951 −0.89535 −0.56261 −0.91968 −1.0234 8.18796E−05 0.999998099 IKBKB_POLA1_PIK3C3 −0.35773 −0.45694 −0.52951 −0.78623 −0.33448 −0.7048 −0.72468 0.127795195 0.454919114 HDAC1_IKBKB_POLA1 −0.43459 −0.35773 −0.45694 −0.43998 −0.98968 −0.78623 −0.75484 0.173191656 0.050057628 EGFR_TOP1_TGFB1 −0.26302 −1.04454 −0.29065 −0.89535 −0.

3667 −1.01887 −0.6885 0.109858337 0.260592184 MAP2K1_TOP1_PIK3C3 −0.09528 −1.04454 −0.52951 −0.87661 −0.54595 −0.91968 −0.99044 3.089E−05 0.99970726 ERBB2_POLA1_TGFB1 −0.30289 −0.45694 −0.29065 −0.67235 −0.26734 −0.80145 −0.50254 0.725192331 0.999822124 POLA1_TOP1_FGF2 −0.45694 −1.04454 −0.05524 −0.83822 −0.69009 −0.81541 −1.12951 0.009711465 0.997153132 MAP2K1_TOP1_TYMS −0.09528 −1.04454 −0.56899 −0.87661 −0.71457 −1.09903 −1.15347 1.73209E−07 0.984860675 IKBKB_TOP1_TGFB1 −0.35773 −1.04454 −0.29065 −0.77903 −0.35915 −1.01887 −0.7943 0.096295984 0.626248758 ERBB2_TOP1_TUBA1A −0.30289 −1.04454 −0.25322 −0.74886 −0.55315 −1.10077 −0.98703 0.002900488 0.999658143 EGFR_POLA1_TOP1 −0.26302 −0.45694 −1.04454 −0.

208 −0.89535 −0.83822 −1.0546 0.000677273 0.022158858 HDAC1_POLA1_TGFB1 −0.43459 −0.45694 −0.29065 −0.98968 −0.25654 −0.80145 −0.

6726 0.59411713 0.709821232 DNMT1

TOP1

TGFB1 −0.27582 −1.04454 −0.29065 −0.9299

−0.34998 −1.01887 −0.78029 0.029452358 0.531018964 IKBKB_MTOR_TOP1 −0.35773 −0.71279 −1.04454 −0.77193 −0.77903 −0.84956 −1.20178 0.001889535 0.178084961 ERBB2_TOP1_PIK3C3 −0.30289 −1.04454 −0.52951 −0.74886 −0.50956 −0.91968 −0.93841 0.000487426 0.976850814 HDAC1

MTOR

TYMS −0.43459 −0.71279 −0.56899 −1.00956 −0.74076 −1.0865 −0.96234 0.036182627 0.651935225 DNMT1_TOP1_FGF2 −0.27582 −1.04454 −0.05524 −0.92996 −0.33702 −0.81541 −0.76324 0.026909543 0.426801764 HDAC1_TOP1_PIK3C3 −0.43459 −1.04454 −0.52951 −0.81956 −0.60726 −0.91968 −1.02733 0.004836098 0.999999524 IKBKB_TOP1_TYMS −0.35773 −1.04454 −0.56899 −0.77903 −0.59343 −1.09903 −1.01218 0.000871856 0.999976701 TOP1_TYMS_PIK3C3 −1.04454 −0.56899 −0.52951 −1.09903 −0.91968 −0.63063 −1.04398 1 0.030024958 HDAC1_TOP1_TGFB1 −0.43459 −1.04454 −0.29065 −0.81956 −0.25654 −1.01887 −0.82014 0.146270594 0.690036709 EGFR_HDAC1_TUBA1A −0.26302 −0.43459 −0.25322 −0.45467 −0.60402 −0.48481 −0.40509 0.865194206 0.999963016 HDAC1_MAP2K1_TYMS −0.43459 −0.09528 −0.56899 −0.36008 −0.74076 −0.71457 −0.51557 0.984913992 0.017696873 HDAC1_TOP1_TUBA1A −0.43459 −1.04454 −0.25322 −0.81956 −0.48481 −1.10077 −0.89301 0.068422256 0.926755637 EGFR_ERBB2_TOP1 −0.26302 −0.30289 −1.04454 −0.54353 −0.89535 −0.74886 −0.94505 0.000368552 0.000774547 IKBKB_TUBA1A_PIK3C3 −0.35773 −0.25322 −0.52951 −0.49372 −0.33448 −0.949 −0.65533 0.482509618 0.20051012 DNMT1_IKBKB_TOP1 −0.27582 −0.35773 −1.04454 −0.39718 −0.92996 −0.77903 −0.78549 0.016279404 0.057386138 MTOR_POLA1_TYMS −0.71279 −0.45694 −0.56899 −1.11793 −1.0865 −0.99179 −1.04588 0.518414397 0.063208762 HDAC1_POLA1_TOP1 −0.43459 −0.45694 −1.04454 −0.98968 −0.81956 −0.83822 −1.36941 0.000190026 0.000413231 POLA1_TOP1_TYMS −0.45694 −1.04454 −0.56899 −0.83822 −0.99179 −1.09903 −1.37077 0.000379682 0.497538669 HDAC1_MTOR_POLA1 −0.43459 −0.71279 −0.45694 −1.00956 −0.98968 −1.11793 −1.02115 0.069271672 0.588459847 POLA1_TOP1_PIK3C3 −0.45694 −1.04454 −0.52951 −0.83822 −0.7048 −0.91968 −1.06461 0.034281078 0.999999539 TUBA1A_PIK3C3_TGFB1 −0.25322 −0.52951 −0.29065 −0.949 −0.43878 −0.43419 −0.55154 0.584435924 0.999999281 TOP1_TUBA1A_TGFB1 −1.04454 −0.25322 −0.29065 −1.10077 −1.01887 −0.43878 −0.79319 0.722731545 0.057278786 ERBB2_TOP1_HDAC1 −0.30289 −1.04454 −0.4

459 −0.74886 −0.41417 −0.81956 −0.76678 0.017178234 0.340232637 DNMT1_POLA1_TOP1 −0.27582 −0.45694 −1.04454 −0.58237 −0.92996 −0.83822 −0.92988 0.013952712 0.146731854 MTOR_TUBA1A_TGFB1 −0.71279 −0.25322 −0.29065 −1.01377 −0.91103 −0.43878 −0.60383 0.990156827 0.34032999 MTOR_TOP1_TUBA1A −0.71279 −1.04454 −0.25322 −0.84956 −1.01377 −1.10077 −1.35656 0.074266247 0.680586552 CDK4_ERBB2_MTOR −0.24531 −0.30289 −0.71279 −0.40617 −0.89932 −0.96817 −0.50066 0.610467925 0.792562627 DNMT1_TOP1_TYMS −0.27582 −1.04454 −0.56899 −0.92996 −0.69239 −1.09903 −1.02314 0.000116904 0.999997937 HDAC1_IKBKB_TOP1 −0.43459 −0.35773 −1.04454 −0.43998 −0.81956 −0.77903 −0.76496 0.203980028 0.066077055 HDAC1_MTOR_PIK3C3 −0.43459 −0.71279 −0.52951 −1.00956 −0.60726 −1.25268 −0.96489 0.065014094 0.734222971 CDK4_ERBB2_TOP1 −0.24531 −0.30289 −1.04454 −0.40617 −0.88189 −0.74886 −0.72778 0.032224754 0.059246479 TUBA1A_TYMS_PIK3C3 −0.25322 −0.56899 −0.52951 −0.86356 −0.949 −0.63063 −0.79427 0.049201025 0.786639309 EGFR_TYMS_PIK3C3 −0.26302 −0.56899 −0.52951 −0.83951 −0.56261 −0.63063 −0.64517 0.017341785 0.985033398 CDK4_POLA1_TGFB1 −0.24531 −0.45694 −0.29065 −0.6393 −0.21676 −0.80145 −0.32163 0.996797859 0.945134998 EGFR_IKBKB_TOP1 −0.26302 −0.35773 −1.04454 −0.37936 −0.89535 −0.77903 −0.69367 0.054788281 0.192166916 ERBB2_POLA1_TOP1 −0.30289 −0.45694 −1.04454 −0.67235 −0.74886 −0.83822 −0.98655 0.004102516 0.055760934 CDK4_M

OR_TUBA1A −0.24531 −0.71279 −0.25322 −0.89932 −0.40998 −1.01377 −0.52807 0.48455344 0.850920572 IKBKB_MTOR_PIK3C3 −0.35773 −0.71279 −0.52951 −0.77193 −0.33448 −1.25768 −0.87025 0.035643199 0.9341941

HDAC1_POLA1_PIK3C3 −0.43459 −0.45694 −0.52951 −0.98968 −0.60726 −0.7048 −0.77733 0.189579196 0.273604032 POLA1_TOP1_TUBA1A −0.45694 −1.04454 −0.25322 −0.83822 −0.83211 −1.10077 −1.11585 0.023212634 0.99931756 DNMT1_ERBB2_TOP1 −0.27582 −0.30289 −1.04454 −0.5251 −0.92996 −0.74886 −0.79709 0.007097545 0.010675837 EGFR_MTOR_TOP1 −0.26302 −0.71279 −1.04454 −0.82607 −0.89535 −0.84956 −1.09591 0.002116481 0.386711175 DNMT1_MAP2K1_TOP1 −0.27582 −0.09528 −1.04454 −0.49617 −0.92996 −0.87661 −0.76132 0.04557059 0.002488007 HDAC1_TOP1_TYMS −0.43459 −1.04454 −0.56899 −0.81956 −0.74076 −1.09903 −1.00549 0.004058208 0.999917617 MTOR_

YMS_PIK3C3 −0.71279 −0.56899 −0.52951 −1.0865 −1.25268 −0.63063 −1.03265 0.433741043 0.093025182 MTOR_TOP1_FGF2 −0.71279 −1.04454 −0.05524 −0.84956 −0.82289 −0.81541 −1.06648 0.460826083 0.999999415 EGFR_HDAC1_TYMS −0.26302 −0.43459 −0.56899 −0.45467 −0.83951 −0.74076 −0.47206 0.453816985 0.999716871 EGFR_HDAC1_TOP1 −0.26302 −0.43459 −1.04454 −0.45467 −0.89535 −0.81956 −0.67755 0.067882519 0.510024115 MTOR_TOP1_TYMS −0.71279 −1.04454 −0.56899 −0.84956 −1.0865 −1.09903 −1.30696 0.054089606 0.716848015 ERBB2_MTOR_

OP1 −0.30289 −0.71279 −1.04454 −0.96817 −0.74886 −0.84956 −1.18142 0.000225227 0.151058859 IKBKB_

OP

_POLA1 −0.35773 −1.04454 −0.45694 −0.77903 −0.78623 −0.83822 −0.99813 0.007287135 0.999905922 TOP1_TUBA1A_TYMS 1.04454 0.25322 0.56899 1.10077 1.09903

.86356 1.07202 0.999994051 0.000178308 DNMT1_EGFR_TOP1 −0.27582 −0.26302 −1.04454 −0.47204 −0.92996 −0.89535 −0.66998 0.095256823 0.079136015 POLA1_

OP1_

GFB1 −0.45694 −1.04454 −0.29065 −0.83822 −0.80145 −1.01887 −0.9847 0.090735758 0.999706535 TOP1_FGF2_PIK3C3 −1.04454 −0.05524 −0.52951 −0.81541 −0.91968 −0.58806 −0.77116 0.464722774 0.000210337 CDK4_POLA1_TOP1 −0.24531 −0.45694 −1.04454 −0.6393 −0.88189 −0.83822 −0.81836 0.036372544 0.330634884 TOP1_TUBA1A_PIK3C3 −1.04454 −0.25322 −0.52951 −1.10077 −0.91968 −0.949 −1.10494 0.999879174 0.003009138 TOP1_TUBA1A_FGF2 −1.04454 −0.25322 −0.05524 −1.10077 −0.81541 −0.69614 −0.83431 0.809127524 0.019943548 CDK4_TOP1_MTOR −0.24531 −1.04454 −0.71279 −0.88189 −0.89932 −0.84956 −1.03719 0.004727153 0.999999999 EGFR_TOP1_TYMS −0.26302 −1.04454 −0.56899 −0.89535 −0.83951 −1.09903 −0.96291 0.000473581 0.995716814 MTOR_TOP1_

GFB1 −0.71279 −1.04454 −0.29065 −0.84956 −0.91103 −1.01887 −0.95912 0.806761928 0.998484838 MAP2K1_MTOR_TOP1 0.09528 0.71279 1.04454 0.82537 0.87661 0.84956 0.86721 0.005191251 0.969738455 MAP2K1_POLA1_TOP1 −0.09528 −0.45694 −1.04454 −0.6668 −0.87661 −0.83822 −0.70582 0.023989089 0.720749406 HDAC1_MTOR_TOP1 −0.43459 −0.71279 −1.04454 −1.00956 −0.81956 −0.84956 −0.8342 0.253820256 0.986621145 MTOR_TOP1_PIK3C3 −0.71279 −1.04454 −0.52951 −0.84956 −1.25268 −0.91968 −1.00902 0.670529106 0.999991286 Dunnett test adjusted p-value GI scores C vs A + B + C A + B vs A + B + C A + C vs A + B + C B + C vs A + B + C (A, B) + C (A, C) + B (B, C) + A GI_3 score DNMT1_EGFR_POLA1 0.00181165 9.59269E−05 0.002631206 0.009054098 −0.20018 −0.28376 −0.23253 −0.23961 DNMT1_POLA1_ERBB2 1.40718E−05 0.001321999 0.000246371 0.01269297 −0.27251 −0.17583 −0.20969 −0.22042 CDK4_MAP2K1_POLA1 0.000830561 9.92872E−13 0.009979521 0.023613512 −0.51906 −0.31977 −0.14223 −0.3453 DNMT1_MAP2K1_POLA1 0.007011148 0.001157563 0.013175112 0.091891726 −0.0666 −0.34206 −0.07708 −0.17242 CDK4_EGFR_MAP2K1 0.00705591 0.020240228 0.000244301 0.05552559 −0.23778 −0.21674 −0.04682 −0.17132 ERBB2_MAP2K1_POLA1 0.010586817 7.30391E−06 0.145154293 0.146879278 −0.21154 −0.21233 −0.01028 −0.14975 CDK4_MAP2K1_MTOR 0.258788563 8.9109E−09 0.80990169 0.471931554 −0.283

4 −0.0

038 −0.00429 −0.13121 DNMT1_FRBB2_FGF2 1.14707E−05 0.866430527 0.021477463 0.009052311 −0.03649 0.02308 −0.0245 −0.01797 CDK4_EGFR_POLA1 0.0850

5879 4.80103E−05 0.419454941 0.362951194 −0.19654 0.023789 −0.01242 −0.06693 CDK4_POLA1_TYMS 0.00507748 0.003322762 0.00087036

0.609989211 −0.002

7 −0.15406 0.026144 −0.04692 CDK4_DNMT1_MTOR 0.11446398 2.82362E−07 0.501206805 0.131857539 −0.14229 0.028886 −0.11171 −0.07795 MAP2K1_POLA1_TUBA1A 0.001726071 0.505279881 0.006646104 0.99764932 0.024779 −0.04787 0.032144 0.002357 CDK4_MAP2K1_TGFB1 0.67980124 0.013966945 0.204125217 0.492709536 −0.13015 −0.187

0.03473 −0.09891 DNMT1_POLA1_FGF2 1.12773E−06 0.076968632 0.000184161 0.389561362 −0.28296 −0.1266

0.04534 −0.1317 M

OR_POLA1_FGF2 4.41995E−07 0.779043293 0.069615602 0.00909012 −0.17499 −0.0

834 0.054706 −0.06757 EGFR_ERBB2_FGF2 0.000928505 0.9999999 0.120817864 0.156724979 0.062926 0.069163 0.043684 0.058536 DNMT1_EGFR_FGF2 0.001186623 0.988618211 0.28628641 0.137494388 −0.00325 0.069509 0.047409 0.037437 DNMT1_FGF2_

GFB1 0.238284384 0.258671276 0.307677709 0.036501456 0.075052 −0.1474 −0.03055 −0.03861 CDK4_EGFR_FGF2 0.007114587 0.101467828 0.020317991 0.440665876 −0.18785 −0.04794 0.07929 −0.05851 IKBKB_POLA1_TYMS 0.000337887 0.004507311 2.91803E−05 0.243668055 0.079888 −0.2249

0.074196 −0.03485 FGFR_IKBKB_MTOR 0.143100881 5.46063E−06 0.277891298 0.138744426 −0.01135 0.080305 −0.06855 −0.00173 HDAC1_FGF2_TGFB1 0.139667153 0.092859382 0.023408209 0.015783467 0.011835 −0.28482 0.084238 −0.07768 DNMT1_ERBB2_MTOR 0.097971375 0.000231027 0.10693702 0.719636605 0.079204 −0.05656 0.085318 0.030187 MAP2K1_MTOR_IYMS 0.000480841 0.013478088 0.001175229 0.480396879 0.0559

3 0.088963 −0.15661 −0.01017 DNMT1_HDAC1_PIK3C3 0.031234388 0.000433442 0.004271499 0.047068456 0.091897 0.065585 −0.01024 0.048503 ERBB2_MAP2K1_TUBA1A 0.119520653 0.117192648 0.999123609 0.440923185 −0.03387 0.049846 0.094747 0.035518 CDK4_ERBB2_POLA1 0.121337543 0.011376018 0.552786205 0.72165731 0.016422 0.095495 0.070976 0.060445 DNMT1_HDAC1_MAP2K1 3.27602E−06 0.00686695 0.020729967 0.000474695 −0.28292 0.09

856 −0.19799 −0.14237 EGFR_MAP2K1_POLA1 0.131973114 0.000413991 0.533248212 0.761151791 −0.10993 −0.11676 0.096982 −0.04815 CDK4

MAP2K1

TUBA1A 0.203279888 0.00072493 0.792805447 0.704666891 −0.20636 −0.03267 0.097825 −0.05541 CDK4_IKBKB_MAP2K1 0.054708

88 0.999581168 0.0052

6263 0.48

264603 0.0661

6 0.035082 0.099395 0.066564 EGFR_MTOR_FGF2 9.15449E−06 0.854728656 0.000200834 0.858131788 −0.10424 0.029354 0.100363 0.004843 CDK4_HDAC1_TGFB1 0.327136446 0.580219416 0.047637621 0.09939048 0.111

8 0.092897 −0.05661 0.046528 EGFR_HDAC1_FGF2 0.000159312 0.48015472 0.02211193 0.035791595 −0.114

4 0.112457 −0.04345 −0.01956 ERBB2_MAP2K1_TGFB1 0.503664503 0.414576418 0.210920704 0.310030286 0.114641 −0.12487 0.103956 0.02499 POLA1_TUBA1A_FGF2 7.45602E−07 0.663033386 0.13263556

0.140691627 −0.15091 −0.09495 0.114823 −0.05025 DNMT1_TYMS_FGF2 8.51049E−07 0.924856028 0.000650401 0.456801642 −0.04074 0.117636 0.098713 0.056103 DNMT1_EGFR_ERBB2 0.03572984 0.259909161 0.533983216 0.646193599 0.075308 0.088504 0.119734 0.094358 EGFR_IKBKB_TGFB1 0.309776668 0.548239879 0.049003215 0.430005806 0.119786 0.04417

0.071951 0.078187 EGFR_MAP2K1_MTOR 0.692941814 0.000985128 0.93786254

0.937813053 0.014422 −0.04298 0.124056 0.029537 DNMT1_POLA1_TUBA1A 0.000350577 0.04904108 0.052471731 0.867207726 −0.14708 0.064512 0.125267 0.007176 DNMT1_MAP2K1_FGF2 0.00562221 0.995104611 0.759983529 0.572248407 0.101782 −0.01733 0.138861 0.072321 MAP2K1_POLA1_PIK3C3 0.019199421 0.084610241 0.005898765 0.116546184 0.140305 −0.05311 −0.25593 −0.07037 CDK4_ERBB2_FGF2 0.015777386 0.999998578 0.053007844 0.831017399 0.043646 0.042294 0.144047 0.075629 DNMT1_TUBA1A_FGF2 2.43748E−06 0.258513254 0.000756311 0.820624163 −0.18214 −0.23739 0.144339 −0.10633 CDK4_DNMT1_FGF2 0.004920582 0.46409094 0.018857712 0.82592173 −0.08829 −0.00172 0.147614 0.014617 DNMT1_IKBKB_POLA1 0.036538194 0.000753997 0.082679149 0.8761973 −0.06015 0.025833 0.147785 0.034346 MAP2K1_TUBA1A_TYMS 0.30215344 0.00234321 0.905431579 0.997909655 0.144216 0.15258

0.14363 0.146802 HDAC1_MAP2K1_TGFB1 0.359441716 0.498978479 0.121446125 0.200192662 0.08539 −0.21353 0.157809 −0.0039 DNMT1_MTOR_MAP2K1 2.14736E−06 0.391598963 0.002239362 0.538218522 −0.16413 0.160313 0.052552 0.006901 CDK4_DNMT1_IKRKB 0.7649

9653 0.17542979 0.69915015

0.869774472 0.161509 0.160317 0.15509 0.158968 EGFR_IKBKB_TUBA1A 0.002171188 0.004658383 0.506865181 0.085091725 −0.16575 0.163417 −0.04

59 −0.02382 ERBB2_HDAC1_MAP2K1 0.005557984 0.576599137 0.108980394 0.289917777 −0.06724 0.169385 0.086282 0.058173 DNMT1_IKBKB_FGF2 0.000453834 0.64100059 0.251545752 0.04944889 −0.06916 0.173169 0.02865 0.039525 POLA1_FGF2_PIK3C3 0.023114639 0.111439039 0.134029527 0.014541873 0.174589 −0.28496 −1.92E−06 −0.05651 ERBB2_POLA1_MTOR 0.080840888 0.017893737 0.496572325 0.963554974 0.134919 0.174892 0.170599 0.159997 POLA1_FGF2_TGFB1 0.029948079 0.956120181 1 0.003248002 0.176698 0.05265 −0.10085 0.036557 EGFR_FGF2_TGFB1 0.896811491 0.853449673 0.447048843 0.506529668 0.179043 −0.12182 0.095542 0.042912 ERBB2_TYMS_TGFB1 0.025781151 0.192425095 0.002473261 0.831485934 0.04

792 0.146928 0.1

1389 0.124633 DNMT1_POLA1_PIK3C3 0.147889554 0.148208856 0.051729251 0.558545509 0.18185 0.052223 0.050598 0.093207 EGFR_MAP2K1_TUBA1A 0.401218987 0.268017239 0.978443447 0.891037506 0.003312 0.183414 0.13758 0.105397 CDK4_DNMT1_TOP1 0.982035284 5.03284E−08 0.318363581 0.502367046 0.185473 0.007465 0.025025 0.069758 EGFR_FGF2_PIK3C3 0.902794348 0.022266906 0.931482379 0.981991994 0.166974 −0.0468 0.186435 0.096891 ERBB2_IKBKB_MAP2K1 0.021984398 0.14725521 0.422170377 0.167570443 −0.13627 0.186514 0.07526 0.03289 ERBB2_POLA1_HGF2 9.18412E−06 0.848751627 0.000892891 0.906778261 −0.07645 −0.0306 0.188927 0.021031 DNMT1_HDAC1_IKBKB 0.122818958 0.324258157 0.101806555 0.261977723 0.170675 0.189011 0.073044 0.143089 EGFR_ERBB2_POLA1 0.192819548 0.262684775 0.662810485 0.874728203 0.189844 0.113071 0.124755 0.142064 ERBB2_IKBKB_FGF2 0.001881374 0.082337936 0.336946611 0.141096899 −0.17794 0.189906 0.092965 0.022526 CDK4_HDAC1_FGF2 0.06823462 0.999985731 0.177022176 0.964800986 0.035258 0.192299 0.163627 0.128277 CDK4_MTOR_PIK3C3 0.001516895 0.162475763 1.51252E−05 0.999641253 0.123716 −0.15017 0.192879 0.044389 EGFR_IKBKB_MAP2K1 0.055369659 0.994639161 0.44854997 0.391427982 0.044811 0.193874 0.088268 0.107246 CDK4_EGFR_IGFB1 0.999957991 0.936423095 0.917270043 0.964

7225 0.195661 0.159742 0.161935 0.172332 CDK4_DNM

1_HDAC1 0.958844465 0.12134923 0.582007882 0.967567256 0.1964 0.125934 0.171644 0.164291 DNMT1_MAP2K1_TGFB1 0.155714728 0.935265088 0.185947445 0.057994995 0.197349 −0.14422 −0.02508 −0.00034 DNMT1_LRBB2_TUBA1A 0.015854827 0.56160423 0.91

922389 0.765229772 0.083291 0.198102 0.133942 0.137479

KBKB_POLA1_TUBA1A 0.000137581 0.537437566 0.004695239 0.810176271 0.048035 −0.04075 0.198428 0.064076 MAP2K

_POLA1_FGF2 0.002120819 0.980311424 0.132283375 0.925174605 0.135855 0.183412 0.199175 0.172502 ERBB2_HDAC1_IKBKB 0.272428445 0.398944609 0.005070264 0.597914363 0.199286 0.113125 0.170255 0.160332 DNMT1_EGFR_TUBA1A 0.032160398 0.405222565 0.966294847 0.987610523 0.046005 0.174011 0.200587 0.138151 EGFR_POLA1_PIK3C3 0.106450992 0.207035006 0.065428592 0.45601540

0.200821 0.07006 0.018333 0.093768 DNMT1_MTOR_TYMS 0.003391721 0.04948396 0.006053087 0.955339664 0.155752 0.202699 0.159852 0.172577 HDAC1_IKBKB_TYMS 0.079222741 0.00035041 0.591997136 0.038357589 0.114059 0.203573 0.133114 0.149612 EGFR_POLA1_TUBA1A 0.006360746 0.43264318 0.359802673 0.999093763 −0.01704 0.169885 0.204063 0.114574 CDK4_IKBKB_FGF2 0.084368089 0.978406164 0.338937641 0.995903384 0.111895 0.199663 0.204475 0.171225 CDK4_DNM

1_IGFB1 0.967614396 0.926407736 0.547547097 0.999385621 0.193351 0.104102 0.206802 0.16718 ERBB2_HDAC1_TYMS 0.254903432 0.002059262 0.006204096 0.932492694 0.146423 0.046402 0.206906 0.131286 PO

A1_

UBA1A_TYMS 0.00

311

05 0.147408287 0.663707183 0.2048

7416 0.207771 0.051686 0.127173 0.127077 CDK4_EGFR_ERBB2 0.186533006 0.008893574 0.463351586 0.9994996 −0.05069 0.090566 0.210209 0.078053 HDAC1_MAP2K1_TUBA1A 0.100164845 0.235044121 0.859640744 0.378441395 −0.00097 −0.03419 0.210754 0.053196 EGFR_ERBB2_TUBA1A 0.033662627 0.747933551 0.973399303 0.82547687 0.100745 0.210901 0.120165 0.142946 HDAC1_MAP2K1_MTOR 0.390140283 0.000352011 0.999951731 0.640445729 0.025359 0.057321 0.212447 0.095423

KBKB_FGF2_TGFB1 0.956020149 0.818287687 0.999722707 0.649507608 0.174064 0.023402 0.212983 0.133785 EGFR

TYMS

FG

2 3.52258E−05 0.542301407 0.005665881 0.985876443 0.21845 0.194802 0.19798 0.203699 HDAC1_POLA1_TUBA1A 0.000246261 0.998961081 0.006046881 0.644419471 0.196557 −0.1046 0.220355 0.093484 CDK4_HDAC1_MAP2K1 0.254592808 0.999999997 0.07558983

0.9999

7485 0.090047 0.128216 0.22068 0.14502 LRBB2_P

K3C3_

0.203623464 0.985899487 0.054463637 0.72012341 0.221559 0.218199 0.158420 0.199041

GFR_POLA1_FGF2 0.000128386 0.941560811 0.006706841 0.999651746 −0.05325 0.029761 0.223812 0.060626 MAP2K1_TUBA1A_TGFB1 0.754462077 0.992115278 0.609731978 0.999996568 0.224724 0.085419 0.077692 0.12731 ERBB2_TYMS_FGF2 1.28724E−05 0.138387301 0.003703649 0.962505

45 −0.18514 0.196569 0.225225 0.061076 MTOR_TUBA1A_TYMS 0.00029727

0.262162773 0.405452278 0.021793632 0.225365 −0.01766 0.21896

0.13

333 ERBB2_MAP2K1_FGF2 0.02899371 0.938054319 0.953985044 0.944702595 −0.02246 0.022592 0.22636 0.070248 EGFR_IKBKB_POLA1 0.174250117 0.012406474 0.621857732 0.999920757 0.018068 0.160304 0.23102 0.132934 EGFR_HDAC1_MAP2K1 0.036084352 0.999997186 0.281054923 0.861979614 0.080715 0.231329 0.153874 0.153669 MAP2K

_TUBA1A_FGF2 0.006750089 0.668153618 0.248348744 0.805971914 −0.11183 0.008377 0.233914 0.033876 CDK4_FGF2_

GFB1 0.9998171 1.887476225 0.998718606 0.99999938 0.190929 0.015105 0.23466 0.142829 HDAC1_IKBKB_MAP2K1 0.017915467 0.998140067 0.754760143 0.153084003 0.052696 0.23525 0.207099 0.162162 IKBKB_MAP2K1_MTOR 0.705973528 0.000107981 0.79804217 0.95196263 0.020688 −0.07997 0.235927 0.050904 DNMT1_MTOR_FGF2 2.77319E−05 0.994514625 0.002501245 0.999841231 −0.01768 0.187645 0.236555 0.129927 DNMT1_TYMS_TGFB1 0.015495242 0.997487411 0.011204014 0.576211367 0.236857 0.172783 0.097553 0.167672 ERBB2_IKBKB_TUBA1A 0.021954575 0.002751207 0.861226056 0.511092425 −0.16929 0.237216 0.122947 0.048942 POLA

_TUBA1A_IGFB1 0.015989052 0.999598327 0.995335606 0.071358557 0.237702 0.169608 0.010657 0.135238 EGFR_MTOR_TGFB1 0.009314697 0.978522395 0.000501171 0.9999964

0.18086

0.013595 0.238193 0.140122 MAP2K

_TYMS_FGF2 8.49171E−06 0.964228919 0.005599365 0.999460847 0.12676 0.238598 0.063487 0.140682 CDK4_IKBKB_MTOR 0.445637647 0.000483082 0.963486248 0.503826349 0.06643 0.238794 −0.00101 0.096891 DNMT1_MTOR_POLA1 0.009334715 0.23562122 0.014622817 0.9999

3182 0.091605 0.140585 0.2

9186 0.155518 IKBKB_POLA1_TGFB1 0.026902299 0.962341394 0.017045562 0.9862

4045 0.157749 −0.10304 0.240048 0.087951 MTOR_FGF2_PIK3C3 0.049131903 0.535067281 0.953682021 0.031059054 0.240202 0.195721 0.188653 0.207970 MTOR_FGF2_TGFB1 0.019676122 0.999727698 0.999945664 0.0016

0635 0.241348 0.094074 0.086838 0.138593 EGFR_ERBB2_MAP2K1 0.098228717 0.565130326 0.66441581 0.924105584 0.241398 0.171452 0.1771 0.196234 CDK4_EGFR_MTOR 0.853971146 0.001051196 0.999998611 0.991398216 0.017165 0.241666 0.15071 0.132715 MAP2K

_TYMS_TGFB1 0.003267638 0.997542285 0.000327709 0.368577427 0.242811 0.095142 −0.09922 0.07028 HDAC1_TYMS_TGFB1 0.005091331 0.998558404 0.000263659 0.335609039 0.243296 0.037417 0.214389 0.161347 DNMT1_FGF2_PIK3C3 0.965779917 0.052144492 0.899011291 0.999523258 0.244479 −0.04149 0.24184 0.139942 POLA1_TYMS_

G

2 2.89078E−07 0.999993441 0.138846848 0.032117581 0.033159 0.245198 0.054323 0.106946 DNMT1_IKBKB_TYMS 0.330074562 0.00121721 0.843622017 0.249552996 0.162047 0.245992 0.065135 0.155352 DNMT1_POLA1_TYMS 0.108392238 0.046878507 0.216537657 0.999983578 0.130236 0.128202 0.246496 0.167031 HDAC1_IKBKB_FGF2 0.00223598 0.999919 0.480869846 0.196750911 0.033287 0.213576 0.24706 0.160714 EGFR_MAP2K1_TGFB1 0.99999537 0.99820768 0.973546659 0.999976222 0.247259 0.022581 0.242223 0.165784 EGFR_IKBKB_FGF2 0.009743796 0.999050141 0.730729214 0.502599533 0.022466 0.247713 0.125293 0.128088 ERBB2_HDAC1_FGF2 0.00099889 0.891953584 0.23749115 0.262732401 −0.03323 0.248457 0.118032 0.105056 ERBB2_FGF2_TGFB1 0.9903

8028 0.997902766 0.91144522 0.798828304 0.248517 −0.03605 0.190496 0.12735 MAP2K1_PIK3C3_TGFB1 0.303559125 0.99961238 0.149423445 0.782592702 0.248981 0.230445 −0.05815 0.131183 DNMT1_MAP2K1_TUBA1A 0.314480275 0.999999999 0.944187221 0.884352678 0.249162 0.185294 0.166036 0.199644 EG

R_POLA1_TGFB1 0.018223754 0.696921308 0.000875552 0.999999926 0.098577 −0.11927 0.251591 0.065887 MAP2K1_MTOR_FGF2 0.001036392 0.999395524 0.023242567 0.999589701 0.108018 0.252857 0.145578 0.167233 HDAC1_MAP2K1_FGF2 0.007751669 0.748214815 0.473421721 0.430754754 −0.0758 −0.07807 0.256122 0.022895 EGFR_HDAC1_

G

B1 0.545536688 0.999691775 0.145124219 0.220591645 0.257083 0.183018 0.031323 0.153232 CDK4_ERBB2_TUBA1A 0.262019661 0.80262888 0.827883032 0.999999545 0.118834 0.172304 0.257897 0.181636 POLA1_

YMS_TGFB1 0.000223578 0.962578313 0.349657623 0.009499845 0.172245 0.260236 −0.08535 0.10554 HDAC1_MAP2K1_POLA1 0.117326514 0.005542615 0.830135769 0.72210954 −0.02356 0.244374 0.260807 0.152784 MAP2K1_FGF2_PIK3C3 0.9990868 0.134911938 0.999723509 0.999999975 0.26124 0.020268 0.102413 0.123618 HDAC1_TUBA1A_TGFB1 0.189732804 0.885376771 0.05032

485 0.699202128 0.165104 −0.1006 0.263013 0.097933 IKBKB_MAP2K1_TGFB1 0.976713509 0.80113899 0.999986263 0.943700607 0.167313 0.07602 0.267882 0.167783 EGFR_ERBB2_MTOR 0.578801614 0.037935965 0.859796836 0.999998701 0.269169 0.141815 0.244053 0.217077 CDK4_ERBB2_MAP2K1 0.459326422 0.696461042 0.175359256 0.999783027 0.216532 0.096309 0.271877 0.192616 DNMT1_EGFR_TGF

1 0.620813224 0.9999

4099 0.769114329 0.10633242 0.272269 0.122577 0.02207 0.13438 CDK4_IKBKB_TYMS 0.862020336 0.007284535 0.909051301 0.882902752 0.256439 0.273243 0.1543 0.226847 ERBB2_POLA1_

YMS 0.066890798 0.130103432 0.001314444 0.999971204 0.219986 −0.11587 0.273325 0.111569 DNMT1_POLA1_TGFB1 0.033552831 0.577514587 0.027427635 1 0.069435 0.003327 0.273685 0.109736 ERBB2_POLA1_PIK3C3 0.124688216 0.409194401 0.029798107 0.525443964 0.27376 0.038399 0.079587 0.126082 DNMT1_HDAC1_FGF2 0.001276036 0.997488316 0.414402077 0.296732215 0.014188 0.274849 0.096846 0.123503 ERBB2_IKBKB_TYMS 0.997712022 0.002250634 0.389497694 0.999822485 0.199483 0.185623 0.275668 0.219625 HDAC1_MTOR_FGF2 1.83394E−05 0.999988081 0.000600866 0.886837196 0.084754 0.050528 0.277441 0.133339 DNMT1_EGFR_MTOR 0.822893463 0.03226

46 0.955500716 0.99242761 0.277702 0.145137 0.194775 0.204641 DNMT1_PIK3C3_TGFB1 0.170429338 0.979668821 0.187214725 0.614074025 0.214329 0.277848 0.108385 0.198125 DNMT1_IKBKB_PIK3C3 0.887828266 0.092914718 0.741469302 0.020776057 0.277966 0.234318 −0.03842 0.148975 CDK4_TYMS_TGFB1 0.10157012 0.999998971 0.005756872 0.998517638 0.277999 0.173139 0.200608 0.216449 DNMT1_IKBKB_MTOR 0.907047657 0.006433574 0.991446642 0.976075628 0.241714 0.278712 0.179496 0.232623 CDK4_TUBA1A_IGFB1 0.908416995 0.999999768 0.441228294 0.99999679 0.279786 0.049141 0.263249 0.192578 MTOR_

UBA1A_FGF2 1.06521E−06 0.985704785 0.363287099 0.065262874 −0.05933 −0.05222 0.280593 0.045167 EGFR_MAP2K1_FGF2 0.2

30

2397 0.999720219 0.999999927 0.999984357 0.026304 0.102488 0.280777 0.131639 MAP2K1_MTOR_TGFB1 0.02451961 0.999999984 0.007287758 0.996123333 0.281874 0.167204 0.17216 0.205942 ERBB2_IKBKB_POLA1 0.181174177 0.000315647 0.876652576 0.999994296 −0.09818 0.223819 0.28285 0.122892 CDK4_MAP2K1_FGF2 0.19413739 0.135019462 0.644799032 0.997303835 −0.14093 −0.02205 0.283465 0.025439 EGFR_HDAC1_IKBKB 0.447317694 0.929333813 0.383183879 0.859032879 0.282064 0.283615 0.172669 0.245011 IKBKB_

YMS_FGF2 4.91011E−06 0.9097595 0.000478693 0.964380018 −0.03612 0.158596 0.284193 0.127703 CDK4_MTOR_FGF2 0.00103118 0.970811973 0.000955174 0.999901047 0.172146 0.087549 0.28579 0.179054 DNMT1_IKBKB_TGFB1 0.870575954 0.999944455 0.979251365 0.989303947 0.266271 0.286141 0.213415 0.254897 IKBKB_MAP2K1_TUBA1A 0.450008884 0.285616793 0.99957152 0.981604119 0.048524 0.129228 0.288398 0.151163 DNMT1_IKBKB_TUBA1A 0.009129972 0.0570901 0.97457363 0.461771172 −0.00879 0.288782 0.110354 0.123577 DNMT1_MTOR_PIK3C3 0.001533063 0.045395252 7.9

2E−05 0.999999823 0.079308 −0.00134 0.289065 0.115868 EGFR_MAP2K1_PIK3C3 0.999999843 0.166064593 0.998690785 0.999917145 0.277675 0.140087 0.291175 0.234377 DNMT1_MTOR_

G

1 0.009619115 0.980348216 0.005474853 0.999999025 0.187778 0.17065 0.294742 0.216509 CDK4_IKBKB_POLA1 0.35757215 0.030293628 0.964625875 0.998407158 0.093686 0.261879 0.29639 0.213991 CDK4_M

OR_POLA1 0.040323774 0.91011284 0.146428561 0.999797852 0.28944 0.285268 0.296429 0.290371 DNMT1_TUBA1A_TYMS 0.210080267 0.131828413 0.587437342 1 0.297602 0.083978 0.277758 0.215823 ERBB2_TYMS_PIK3C3 0.245104862 0.016221509 0.069952899 0.592083064 0.197488 0.297983 0.152952 0.214648 CDK4_TYMS_FGF2 0.001

5009 0.998788743 0.003418048 0.995630225 0.097064 0.168027 0.298435 0.184955 CDK4_EGFR_HDAC1 0.99990515 0.50

213107 0.999983924 0.99

2

3838 0.259107 0.241971 0.299445 0.266614 CDK4

DNM

1_TUBA1A 0.197055926 0.161380916 0.809855638 0.991409527 0.014269 0.155666 0.305418 0.152334 EGFR_TUBA1A_FGF2 0.001297707 0.99897533 0.047612918 0.999488638 0.005778 −0.09814 0.305685 0.058018 EGFR_ERBB2_HDAC1 0.265532432 0.689641551 0.178115978 0.069935034 0.307101 0.08654 0.006176 0.126358 EGFR_HDAC1_PIK3C3 0.735851246 0.199021677 0.77177737 0.959464463 0.294142 0.307169 0.180246 0.259202 DNMT1_HDAC1_MTOR 0.496222903 0.002049651 0.672498764 0.999965095 0.190484 0.245818 0.307369 0.246978 DNMT1_EGFR_MAP2K1 0.044391454 0.999842932 0.994554447 0.371139071 0.122595 0.314469 0.097075 0.174185 CDK4_POLA1_PIK3C3 0.272374828 0.567688379 0.032715974 0.846007038 0.314482 0.044771 0.095789 0.145955 IKBKB_MAP2K1_FGF2 0.030080044 0.76937923 0.886685745 0.994691005 −0.04546 0.013909 0.314617 0.083588 MAP2K1_TUBA1A_PIK3C3 0.870061687 0.269886805 0.824787066 0.655703385 0.194106 0.073337 0.318438 0.191094 FGF2_PIK3C3_TGFB1 0.333635866 0.999924949 0.067936852 0.862765386 0.319359 0.216399 −0.06992 0.142843 IKBKB_

YMS_TGFB1 0.094951992 0.999997008 0.128131209 0.999036079 0.275694 0.319751 0.317247 0.304073 ERBB2_TUBA1A_TYMS 0.359837735 0.170059476 0.0197

8462 0.99999796 0.276083 −0.14428 0.320399 0.129721 CDK4_MTOR_

G

B1 0.096863515 0.999995247 0.019305523 0.999971382 0.321202 0.060781 0.287572 0.

17462 ERBB2_HDAC1_PIK3C3 0.953899428 0.203376123 0.788607225 0.999995678 0.322086 0.32256 0.288553 0.310969 CDK4_DNMT1_PIK3C3 0.999834069 0.228296301 0.991779198 0.99983937 0.322649 0.219939 0.272582 0.271031 DNMT1_HDAC1_TGFB1 0.698099481 0.999999995 0.868099879 0.340302647 0.285374 0.32358 0.071378 0.221539 ERBB2_MAP2K1_PIK3C3 0.999999984 0.289382283 0.999999123 0.999958049 0.319055 0.082903 0.326907 0.237554 DNMT1_ERBB2_TGFB1 0.574641104 0.999416199 0.735080094 0.269894355 0.328531 0.165643 0.055951 0.178131 EGFR_ERBB2_PIK3C3 0.410434397 0.286142404 0.382388584 0.152753827 0.328841 0.121306 0.02839 0.152883 CDK4_TUBA1A_FGF2 0.001654839 0.43635466 0.002804922 0.972989967 −0.14605 −0.20087 0.330186 −0.03175 HDAC1_TYMS_FGF2 1.18391E−05 0.999938525 0.003764198 0.885822423 0.080472 0.171248 0.330328 0.189617 ERBB2_TUBA1A_TGFB1 0.525177372 0.99963962 0.254621902 0.990100264 0.330352 0.007122 0.228221 0.180615 POLA1_TUBA1A_PIK3C3 0.135247179 0.796941385 0.356831457 0.983760584 0.289593 −0.114 0.333913 0.150811 ERBB2_HDAC1_TGFB1 0.98913262 0.997346433 0.915536584 0.874788108 0.339203 0.336317 0.193807 0.287943 ERBB2_IKBKB_MTOR 0.500268142 3.84708E−06 0.999998888 0.566871996 −0.02122 0.340754 0.089664 0.126617 MAP2K1_MTOR_TUBA1A 0.033453983 0.998827061 0.108427005 0.58732653 0.311372 0.336007 0.341828 0.329669 DNMT1_ERBB2_IKBKB 0.527175507 0.999993649 0.581643083 0.030857436 0.342214 0.159456 −0.01364 0.153551 DNMT1_ERBB2_PIK3C3 0.550944046 0.324077131 0.314540423 0.246094849 0.344453 0.118046 0.075232 0.173552 DNMT1_HDAC1_POLA1 0.056305756 0.009456404 0.119764308 0.996531279 −0.00785 0.096462 0.345008 0.135267 ERBB2_MTOR_TYMS 0.009359863 0.623181698 7.11761E−05 0.98002487 0.346073 −0.02976 0.198298 0.161016 ERBB2_IKBKB_PIK3C3 0.999999923 0.028746281 0.999998248 0.244243437 0.259466 0.346101 0.116177 0.236894 HDAC1_POLA1_FGF2 1.86327E−05 0.450472352 0.002447363 0.97106313 0.267609 −0.00259 0.3473

2 0.194302 HDAC1_PIK3C3_TGFB1 0.315968063 0.994768488 0.09473712 0.878737637 0.348623 0.23676 0.319499 0.300754 HDAC1_IKBKB_TUBA1A 0.109235595 0.735717277 0.946491947 0.961823533 0.114342 0.263678 0.34945 0.238618 CDK4_DNMT1_EGFR 0.930124045 0.957643519 0.594423152 0.84284573 0.187052 0.133723 0.350195 0.220275 DNMT1_MAP2K1_TYMS 0.794569484 0.206865024 0.999967129 1 0.350713 0.073222 0.275953 0.227522 CDK4_DNMT1_POLA1 0.974886339 0.228356715 0.991031028 0.99999702 0.183889 0.350889 0.263448 0.264239 CDK4_IKBKB_TUBA1A 0.717258929 0.998472527 0.999999999 0.964307034 0.211029 0.353618 0.324943 0.295038 IKBKB_TOP1_PIK3C3 0.022017783 0.390215269 1.71948E−05 0.961450726 0.284035 0.35452 0.252909 0.296465 CDK4_DNMT1_ERBB2 0.884902049 0.686988808 0.999999626 0.79274309 0.178539 0.266465 0.354877 0.264578 CDK4_HDAC1_IKBKB 0.960664434 0.97503379 0.955

3

647 0.999999292 0.285893 0.355166 0.233972 0.290727 ERBB2_TOP1_TYMS 0.013767231 0.077262223 0.000112186 0.999877233 0.180801 0.356037 0.264871 0.265216 TYMS_FGF2_TGFB1 0.327721769 0.989984035 0.999976968 0.073694699 0.356729 0.077967 0.270052 0.229249 MAP2K1_FGF2_TGFB1 0.998997239 0.978977342 0.997997059 1 0.358634 0.099125 0.096845 0.178777 IKBKB_POLA1_FGF2 0.00024564 0.94665176 0.005830369 1 0.153665 0.043541 0.360012 0.178629 IKBKB_MAP2K1_TYMS 0.712636118 1.94424E−05 0.704324742 1 0.111953 −0.0234 0.360192 0.138855 ERBB2_FGF2_PIK3C3 1 0.194858793 0.999980495 0.987823424 0.317395 0.036186 0.362335 0.229738 IKBKB_TUBA1A_TGFB1 0.87866369 0.996127347 0.985717042 0.999999999 0.350396 0.1784 0.362534 0.294296 CDK4_TOP1_TUBA1A 0.000516484 0.738795212 0.001180993 0.999999979 0.044635 0.36404 0.255605 0.21399 CDK4_MAP2K1_TYMS 0.999938526 2.3559E−06 0.999999997 0.741982808 0.051576 0.099484 0.364129 0.164023 CDK4_EGFR_IKBKB 0.952624735 0.995930023 0.818584777 0.770124452 0.312997 0.365133 0.354885 0.344148 CDK4_EGFR_TUBA1A 0.541254304 0.2282938 0.989762675 0.907717009 −0.00433 0.190396 0.366725 0.174436 DNMT1_EGFR_TYMS 0.663385532 0.085620567 0.995260013 0.941548347 0.293231 0.207613 0.367542 0.287799 DNMT1_HDAC1_TYMS 0.568069679 0.037631358 0.986880202 0.999995361 0.268027 0.370307 0.25991 0.29846 ERBB2_MAP2K1_MTOR 0.999919189 0.030119876 0.659366625 0.997378287 0.267617 0.3068 0.371603 0.314645 CDK4_POLA1_FGF2 0.005891845 0.984692004 0.011724798 0.852652834 0.133136 0.052712 0.373994 0.179032 EGFR_MTOR_POLA1 0.104054722 0.887639376 0.283401799 0.987453646 0.277855 0.328435 0.375799 0.32676 DNMT1_TUBA1A_TGFB1 0.501120619 0.965809947 0.655512216 0.992595469 0.375838 0.09814 0.209548 0.222595 CDK4_ERBB2_IKBKB 0.999892615 0.999964736 0.999993804 0.584468355 0.377416 0.288297 0.109973 0.25352 EGFR_POLA1_TYMS 0.206165845 0.238651329 0.990198843 0.993584765 0.272097 0.378756 0.337121 0.328595 EGFR_HDAC1_POLA1 0.069498803 0.01822827 0.341674302 0.928632113 0.039072 0.182859 0.380169 0.192624 ERBB2_POLA1_TUBA1A 0.022063582 0.9895393 0.60683555 0.991686527 0.172859 0.257368 0.382282 0.267948 EGFR_IKBKB_PIK3C3 0.999999957 0.506769527 0.999912277 0.26108044 0.371043 0.382518 0.059678 0.261727 HDAC1_TUBA1A_FGF2 0.001628144 0.423586958 0.037959768 0.999428167 −0.20755 −0.17659 0.383138 −0.03361 EGFR_TUBA1A_TYMS 0.581219494 0.619481682 0.997726078 0.987632614 0.387508 0.307237 0.341088 0.344877 TUBA1A_FGF2_PIK3C3 0.539805004 0.946872435 0.979854653 0.569595847 0.388961 0.167552 0.004596 0.176664 MAP2K1_POLA1_TGFB1 0.384480197 0.971691658 0.259922688 0.502026356 0.389807 0.177855 0.329079 0.295783 IKBKB_TYMS_PIK3C3 0.40426552 0.627769808 0.000964846 0.858708834 0.391816 0.172342 0.257235 0.270625 CDK4_ERBB2_TYMS 0.999999169 0.443331159 0.999993347 0.719376616 0.391913 0.319599 0.11061 0.268251 EGFR_TOP1_MAP2K1 0.000141151 0.999994365 0.000357082 0.999782383 0.072637 0.392516 0.22164 0.221984 CDK4_POLA1_TUBA1A 0.067241664 0.999577601 0.266498821 0.867279485 0.208276 0.182672 0.393179 0.257995 MAP2K1_POLA1_TYMS 0.380723378 0.705741403 0.885647437 0.798142807 0.395071 0.330789 0.246352 0.322662 DNMT1_TOP1_TUBA1A 1.48133E−06 0.233825081 0.000413246 0.915334592 −0.05545 0.396144 0.137956 0.144879 DNMT1_EGFR_IKBKB 0.987881741 0.999114395 0.999364721 0.994232378 0.396356 0.226793 0.221772 0.279143 EGFR_ERBB2_TGFB1 0.802848436 0.885436325 0.329989475 0.514272003 0.396425 0.1018 0.092615 0.189039 HDAC1_IKBKB_TGFB1 0.942018091 0.998483949 0.69092212 0.999302702 0.334297 0.217933 0.397409 0.314417 CDK4_TUBA1A_TYMS 0.87356149 0.088525553 0.897705408 0.755499224 0.26752 0.141736 0.397429 0.264591 MTOR_TUBA1A_PIK3C3 0.036145178 0.864849625 0.999999989 0.582782406 0.27909 0.241713 0.397601 0.304473 EGFR_ERBB2_TYMS 0.688720512 0.332612041 0.924436196 0.057035726 0.369839 0.399724 −0.03111 0.229313 CDK4_FGF2_PIK3C3 0.974390533 0.123861644 0.999999874 0.656306272 0.253954 0.064668 0.400646 0.231993 DNMT1_ERBB2_TYMS 0.911381416 0.535206754 1 0.175363568 0.401773 0.30296 0.032058 0.235296 DNMT1_IKBKB_MAP2K1 0.027465491 0.992290558 0.995657739 0.247989459 0.043239 0.404675 0.081676 0.165966 ERBB2_MTOR_PIK3C3 0.008203319 0.801645103 0.0006317 0.97980668 0.347184 0.071849 0.405066 0.265957 CDK4_HDAC1_TUBA1A 0.773880321 0.997304194 0.999952173 0.999505532 0.193366 0.405228 0.29078 0.293573 IKBKB_MTOR_FGF2 0.000211483 1 0.003205575 0.999351087 0.053946 0.21397 0.4074 0.2166 IKBKB_MTOR_TYMS 0.035966756 0.31072302 0.013167488 0.999202677 0.304701 0.270006 0.408017 0.3263 TYMS_PIK3C3_TGFB1 0.034941246 0.994626947 0.854464762 0.181979897 0.232101 0.408234 0.314002 0.316151 CDK4_MAP2K1_PIK3C3 0.769453223 0.033809413 0.989372394 0.513194475 0.226126 0.155712 0.409545 0.259374 ERBB2_MTOR_TGFB1 0.019819745 0.960103825 0.00267954 0.998948624 0.410423 0.131729 0.365512 0.296569 POLA1_PIK3C3_TGFB1 0.012529139 0.694184386 0.97923451 0.033008363 0.077422 0.412924 −0.0269 0.139955 CDK4_ERBB2_HDAC1 0.999999991 0.99998111 0.998128564 0.999998899 0.413381 0.254989 0.232099 0.297722 HDAC1_MAP2K1_PIK3C3 0.999870179 0.397518294 0.999339044 0.999988604 0.323112 0.136057 0.414067 0.285747 EGFR_MTO

_TUBA1A 0.009545053 0.997213684 0.385547878 0.984024577 0.179726 0.417235 0.377222 0.320512 TYMS_PIK3C3_FGF2 1.60994

05 0.885329747 0.796394551 0.647967709 −0.05392 0.400975 0.417259 0.233869 EGFR

IKBKB

TYMS 0.38401187 0.000643747 0.985609646 0.313164794 0.16964 0.418534 0.077748 0.21377 CDK4_TOP1_FGF2 0.000158274 0.969857873 0.000127833 0.999895315 0.156256 0.42084 0.27985 0.281109 ERBB2_IKBKB_TOP1 0.839888821 3.70312E−05 0.90231195 0.971187834 0.421783 0.232688 0.20801 0.284061 ERBB2_IKBKB_TGF

1 0.998404423 0.999999064 0.999859166 0.79179712 0.302539 0.385815 0.42278 0.369445 CDK4_TOP1_TGFB1 0.013187382 0.999827954 0.000498672 0.760583876 0.331178 0.419938 0.422817 0.390651 MAP2K1_TOP1_TGFB1 0.040474632 0.999985185 0.011173941 0.989455895 0.257786 0.423626 0.204669 0.292082 MAP2K1_TOP1_FGF2 0.000414724 0.999499745 0.004382483 0.976423899 −0.0016 0.423746 −0.02276 0.11578 DNMT1_ERBB2_MAP2K1 0.188723191 0.593493314 0.780391996 0.986188201 0.245824 0.424501 0.212756 0.291113 IKBKB_

BA1A_TYMS 0.333874764 0.0

9785894 0.

60810292 0.983492067 0.267301 0.051248 0.425885 0.238482 DNMT1_HDAC1_

BA1A 0.041486308 0.610895737 0.999999931 0.833612019 0.111194 0.427098 0.162898 0.226295 ERBB2_TUBA1A_FGF2 0.004308866 0.999996994 0.192631762 0.856830496 0.038051 −0.00061 0.428693 0.140155 ERBB2_MTOR_

BA1A 0.008033094 0.994198177 0.231815445 0.968418951 0.336028 0.380564 0.431287 0.382079 EGFR_

BA1A_

G

1 0.832432453 0.872036409 0.435285031 0.999992024 0.432362 0.027581 0.239495 0.221906 CDK4_ERBB2_PIK3C3 0.999952491 0.892695631 0.987480307 0.999999951 0.433126 0.242489 0.252318 0.306463 CDK4_HDAC1_TYMS 0.999929283 0.283101927 1 0.744406299 0.347832 0.433909 0.385425 0.388609 MAP2K1_M

OR_PIK3C3 0.276226922 0.993198868 0.189299175 0.285823671 0.437391 0.341257 0.43047 0.402346 ERBB2_HDAC1_TUBA1A 0.168150358 0.753462796 0.999999985 0.99235773 0.120693 0.441037 0.240996 0.260794 EGFR_MTOR_PIK3C3 0.044169151 0.580960362 0.018765737 0.826113486 0.28223 0.202049 0.442349 0.305127 DNMT1_HDAC

_

OP1 0.99999994 8.97933E−05 0.890251991 0.457013129 0.444578 0.308885 0.039715 0.252715

RBB2_MAP2K1_TYMS 1 0.063201999 0.738837012 0.617192409 0.30904 −0.02761 0.446026 0.225529 M

OR_POLA1_TUBA1A 0.000974273 0.999997879 0.997824318 0.59605700

0.276295 0.375848 0.450039 0.365527 TUBA1A

FGF2

TGFB1 0.467893769 0.733961996 0.970504938 0.144356887 0.451156 −0.04162 −0.03617 0.1026 CDK4_EGFR_PIK3C3 0.638502055 0.733259539 0.941432828 0.264461565 0.399684 0.350302 0.453048 0.400383 HDAC1_TOP1_

G

2 1.42538E−06 0.985622181 0.000139193 0.969722674 −0.03344 0.45408 0.341762 0.235465

GFR_PIK3C3_TG

B1 0.966483764 0.641606882 0.662567357 0.99974

934 0.455419 0.368329 0.299373 0.372895

GFR_M

OR_TYMS 0.04047064 0.423518172 0.452991282 0.999999992 0.300263 0.457501 0.254726 0.334739 POLA1_

YMS_PIK3C3 0.024997365 0.996653394 0.129793056 0.03627345 0.457545 0.210033 0.023813 0.217718 IKBKB_MTOR_TGFB1 0.027306681 0.999888676 0.022118928 0.985080927 0.251838 0.2612 0.458018 0.320378

UBA1A_

YMS_FGF2 6.48108E−05 0.998539497 0.944517197 0.575987902 0.112045 0.458371 0.057723 0.197073 EGFR_E

BB2_IKBKB 0.96339318 0.828600666 0.977502699 0.231129363 0.459134 0.240

24 0.072048 0.247167 EGFR_MAP2K1_TYMS 0.997763411 0.073590254 0.01380828 0.27066638 0.31725 0.417081 0.459883 0.396777 IKBKB_MTOR_POLA1 0.032848928 0.498357952 0.525147017 0.996583609 0.189851 0.459999 0.436648 0.356434 IKBKB_MAP2K1_POLA1 0.966207615 0.085818253 0.355758124 0.950195325 0.147528 0.317022 0.460049 0.301891 HDAC1_MAP2K1_TOP1 0.989626221 0.001516231 0.961192872 0.997126618 0.462127 −0.02766 0.368706 0.24845 HDAC1_TUBA1A_TYMS 0.284586462 0.033435433 0.94380273 0.99993905 0.21787 0.158049 0.462227 0.272861 EGFR_TOP1_FGF2 2.29871E−05 0.999999901 0.000646031 0.995529502 0.066306 0.462368 0.194147 0.230265 C

K4_DNMT1_MAP2K1 0.465236249 0.99999677 0.172766814 0.115158318 0.107951 0.075655 0.462968 0.203583 MAP2K1_TYMS_PIK3C3 0.305088023 0.989392088 0.213866845 0.657715231 0.463934 0.3348 −0.05424 0.227176 C

K4_MTOR_HDAC1 0.168068455 0.999989376 0.03744796 0.956605494 0.464468 0.222831 0.385426 0.353765 IKBKB_MAP2K1_PIK3C3 0.971296204 0.485417849 0.920828963 0.876814412 0.350441 −0.00438 0.469546 0.254827 CDK4_DNMT1_TYMS 0.938912522 0.359283234 0.667300426 0.169605974 0.392395 0.408007 0.46992 0.423051 DNMT1_EGFR_PIK3C3 1 0.992227466 0.999999995 0.999701326 0.471148 0.257937 0.308039 0.342699 DNMT1

MAP2K1_PIK3C3 0.999989372 0.99483484 0.99990933 0.999999983 0.473126 0.068042 0.269232 0.259282 HDAC1_FGF2_PIK3C3 0.999995609 0.239424931 0.99438371 0.999376814 0.297804 0.113013 0.473168 0.286235 DNMT1_ERBB2_HDAC1 0.997743175 0.998729756 0.99965082 0.967547516 0.473224 0.27213 0.20353 0.311452 HDAC1_MTOR_TGFB1 0.019773572 0.949581829 0.002898563 0.999940655 0.427934 0.097054 0.473347 0.32154 MTOR_POLA1_PIK3C3 0.020400882 0.989721134 0.999999764 0.064043749 0.412058 0.474233 0.182205 0.350114

OP1_FGF2_

GHB1 0.021811352 1 0.652488081 0.001666023 0.290037 0.258081 0.474758 0.337654 CDK4_IKBKB_TGFB1 0.913708202 0.285535059 0.999444916 0.356014722 0.479612 0.391556 0.421529 0.430435 EGFR_HDAC1_MTOR 0.996976731 0.145637393 0.999930032 0.646010996 0.375892 0.4691 0.481013 0.441224 CDK4_TOP1_TYMS 0.003713191 0.249633904 0.000552835 0.996566616 0.287442 0.481062 0.180908 0.310707 CDK4_EGFR_TOP1 0.515441387 0.000810326 0.976051371 0.952105466 0.484215 0.359536 0.355288 0.398427 HDAC1_IKBKB_PIK3C3 0.998375401 0.996611122 0.671442963 0.482034475 0.485479 0.480978 0.28506 0.413989 IKBKB_FGF2_PIK3C3 0.989319927 0.3007066 0.714713241 0.687137327 0.343928 −0.07026 0.485808 0.22904 CDK4_IKBKB_PIK3C3 0.858613493 0.997322577 0.999688353 0.937464407 0.487829 0.386311 0.166216 0.339875 IKBKB_PIK3C3_TGFB1 0.933151978 0.985385486 0.998733207 0.999652285 0.224622 0.488153 0.391416 0.363648 DNMT1_EGFR_HDAC1 0.999975486 0.985402475 0.997143993 0.997630419 0.495815 0.307917 0.319681 0.371857 ERBB2_TOP1_TGFB1 0.008533992 0.990893316 0.000632826 0.626206739 0.213951 0.486323 0.496194 0.392411 CDK4_MTOR_TYMS 0.181073546 0.997237144 0.13256367 0.966590703 0.497133 0.341574 0.36064 0.398104 CDK4_TUBA1A_PIK3C3 0.934363091 0.404204052 0.51904594 0.542864923 0.242384 −0.00172 0.497211 0.229127 IKBKB_MTOR_TUBA1A 0.002534084 0.973036596 0.058450294 0.913666999 0.154517 0.335875 0.500866 0.32282

HDAC1_IKBKB_MTOR 0.931427591 0.038602108 0.923006004 0.984561423 0.286463 0.50098 0.340213 0.372931 HDAC1_POLA1_TYMS 0.043240059 0.997620006 0.195974518 0.997767588 0.502799 0.141822 0.370513 0.329824 CDK4_

OP1_MAP2K1 0.016812454 0.33804159 0.00144374 0.319009928 0.357577 0.503288 0.502332 0.45275 DNMT1_TUBA1A_PIK3C3 0.861974303 0.944272541 0.718467832 0.582423649 0.400175 0.058959 0.50525 0.306843 IKBKB_MAP2K1_TOP1 0.537465521 0.001621255 0.999999951 0.981866117 0.510855 0.085548 0.445585 0.333435

UBA1A_TYMS_TGFB1 0.116794189 0.449909298 0.526188767 0.987083805 0.510867 0.36442 0.177782 0.344043 ERBB2_TOP1_FGF2 9.65811E−06 0.960253923 0.000680355 0.999890306 −0.04392 0.513021 0.270279 0.224841 ERBB2_MAP2K1_TOP1 0.786631441 0.002298976 0.98194591 0.999925216 0.513187 0.001304 0.336663 0.265203 CDK4_PIK3C3_

GFB1 0.997683107 0.318533633 0.999997988 0.375509952 0.50122 0.514682 0.447919 0.487

59 ERBB2_HDAC1_POLA1 0.29212147 0.067415407 0.965886297 0.558313564 0.096121 0.331956 0.517581 0.303667 DNM

1_TYMS_PIK3C3 0.667805248 0.999999627 0.451677925 0.978829088 0.518618 0.391025 0.20318 0.364702 CDK4_TYMS_PIK3C3 0.980624282 0.999999694 0.476710046 0.999972

76 0.519732 0.401409 0.266207 0.391914 EGFR_TOP1_TUBA1A 0.000191791 0.635134718 0.022967892 0.999997723 0.025341 0.525323 0.240559 0.247238 ERBB2_TUBA1A_PIK3C3 0.852894309 0.849911017 0.642135741 0.624127655 0.3566 0.036729 0.5

5834 0.289856 CDK4_HDAC1_TOP1 0.945457798 0.007946595 0.99999951 0.996450817 0.526377 0.418834 0.167224 0.362226 MTOR_POLA1_TGFB1 0.025047246 0.977091969 0.998673086 0.898530717 0.420994 0.380377 0.526644 0.441371 IKBKB_TOP1_

G

2 6.36012E−05 0.999999604 0.00103435 0.999987285 0.042053 0.52673 0.380928 0.299993 CDK4_HDAC1_POLA1 0.684139231 0.236311369 0.998060378 0.437216348 0.128764 0.36623 0.527335 0.330517 DNMT1_TOP1_MTOR 0.035455957 0.182959378 0.033275326 0.122694917 0.341579 0.532606 −0.17578 0.192238 TOP1_TYMS_FGF2 1.22782E−08 0.999990369 0.175983174 0.003657639 0.031778 0.261905 0.533303 0.259158 CDK4_HDAC1_PIK3C3 0.78590804 0.999999992 0.986376052 0.226179851 0.535394 0.503149 0.478971 0.505661 HDAC1_TUBA1A_PIK3C3 0.433507143 0.1827259 0.

41396711 0.983747817 0.166265 0.012429 0.53551 0.219385 ERBB2

MTOR

FGF2 0.019994559 0.100732154 0.301729741 0.553122575 0.433511 0.439385 0.535874 0.468851 EGFR_TYMS_TGFB1 0.19019606 0.23781491 0.024365301 0.999958328 0.536514 0.212004 0.237281 0.320798 CDK4_TOP1_PIK3C3 0.071738536 0.996542957 0.002557228 0.999966291 0.462905 0.538203 0.216498 0.39888 DNMT1_TOP1_PIK3C3 0.011764932 0.959181138 0.001201934 0.935189944 0.429185 0.539566 0.165217 0.368667 HDAC1_TYMS_PIK3C3 0.44575163 0.999999514 0.747799208 0.881881071 0.540138 0.446122 0.335097 0.438001 DNMT1_MTOR_TUBA1A 0.03162233 0.999974733 0.769347908 0.525020766 0.282038 0.542609 0.529172 0.44

12 EGFR_TUBA1A_PIK3C3 0.976049938 0.99931936 0.98534287 0.447489321 0.46759 0.1499 0.546088 0.37

68 CDK4_ERBB2_TGFB1 0.778248872 0.091360092 0.974990979 0.77388591 0.553636 0.376461 0.369469 0.430721 TOP1_PIK3C3_TGFB1 0.000643264 0.994422095 0.999987516 0.001950974 0.217

51 0.555

97 0.485655 0.411575 CDK4_EGFR_TYMS 0.999570629 0.032849069 0.974465596 0.032039456 0.266524 0.335466 0.557308 0.381042 TOP1_TYMS_TGFB1 0.000259174 0.99969127 0.999921687 0.014153716 0.335234 0.533406 0.557996 0.472065 MAP2K1_TOP1_TUBA1A 0.012478425 1 0.03272339 0.670249267 0.253186 0.55833 0.319401 0.370936 IKBKB_TUBA1A_FGF2 0.00826512 0.99999999 0.23825042 0.29889969 0.06105 0.039715 0.56596 0.199896 IKBKB_TOP1_TUBA1A 0.000862616 0.695364072 0.016912567 0.936458763 0.060072 0.566083 0.486324 0.351309 MTOR_PIK3C3_TGFB1 0.0131819 0.516286434 0.999454764 0.032287399 0.569123 0.466331 0.172777 0.392199 MTOR_PO

A1_TOP1 0.206702466 0.264684082 0.037923207 0.024965411 0.572906 −0.28306 −0.03856 0.02731 CDK4_IKBKB_TOP1 0.698797215 0.002554372 0.999712464 0.996101296 0.574547 0.397731 0.182449 0.375479 MTOR

YMS

FGF2 0.000438601 0.424575582 0.999999998 0.649458938 0.325246 0.575383 0.50755 0.465497 HDAC1_MTOR_TUBA1A 0.008379026 0.943547266 0.111154759 0.945558843 0.39018 0.324999 0.575763 0.426459 ERBB2_HDAC1_MTOR 0.981794051 0.040430325 0.388262153 0.778717025 0.302343 0.578151 0.487828 0.451473 MTOR_TYMS_TGFB1 0.013597415 0.803393587 0.999999987 0.240275348 0.47547 0.578334 0.379012 0.475364 MAP2K1_MTOR_POLA1 0.448904157 0.999991193 0.966031457 0.423138947 0.485531 0.582814 0.416435 0.493377 EGFR_TOP1_PIK3C3 0.020881863 0.904207323 0.007388811 0.960508368 0.401455 0.583746 0.159295 0.370312 IKBKB_POLA1_PIK3C3 0.723266395 0.996671013 0.028109341 0.999995399 0.59105 0.066733 0.337846 0.314363 HDAC1_IKBKB_POLA1 0.254944046 0.085840192 0.356958965 0.999877797 0.142082 0.592574 0.46598 0.386

76 EGFR_TOP1_TGFB1 0.143794455 0.636168733 0.02492707 0.201764508 0.497504 0.592704 0.59339 0.560541 MAP2K1_TOP1_PIK3C3 0.071125482 0.957765517 0.031468671 0.996415394 0.415679 0.600055 0.024516 0.323954 ERBB2_POLA1_TGFB1 0.674087764 0.764153931 0.414782886 0.270872802 0.46046 0.221739 0.60179 0.419138 POLA1_TOP1_FGF2 2.22936E−06 0.436969636 0.079455973 0.315481059 −0.23606 0.60511 0.142837 0.119052 MAP2K1_TOP1_TYMS 0.010137775 0.298038945 0.028504895 0.999075166 0.292127 0.605637 0.040839 0.292544 IKBKB_TOP1_TGFB1 0.039133959 0.999999524 0.034952268 0.586859587 0.275373 0.609388 0.582294 0.480909 ERBB2_TOP1_TUBA1A 0.001416002 0.555895176 0.061292898 0.973290253 0.015054 0.610656 0.416628 0.323069 EGFR_POLA1_TOP1 0.999999989 0.08340579 0.877664525 0.704023

04 0.610744 0.297692 0.046641 0.298171 HDAC1_POLA1_TGFB1 0.136216577 0.184162738 0.03412277 0.916444027 0.613073 0.046217 0.568777 0.383393 DNMT1

TOP1

TGFB1 0.033715335 0.85361931 0.026011542 0.478059044 0.440324 0.614224 0.514403 0.521324 IKBKB_MTOR_TOP1 0.961318057 0.174220474 0.179502663 0.42146259 0.614686 0.290032 0.005514 0.279456 ERBB2_TOP1_PIK3C3 0.054260172 0.586435945 0.007918558 0.999995983 0.339955 0.615686 0.284152 0.406

16 HDAC1

MTOR

TYMS 0.193816973 0.999786395 0.611199842 0.953818158 0.616203 0.491201 0.558752 0.554544 DNMT1_TOP1_FGF2 0.000274691 0.755568368 0.019214621 0.998873613 0.221962 0.618316 0.327995 0.379661 HDAC1_TOP1_PIK3C3 0.023625245 0.667845182 0.02325665 0.958877828 0.321735 0.624456 0.325938 0.417649 IKBKB_TOP1_TYMS 0.058712932 0.44043831 0.023014666 0.984529519 0.335837 0.625795 0.444585 0.463932 TOP1_TYMS_PIK3C3 0.012103041 0.998373361 0.904247191 0.020610425 0.584557 0.444682 0.63118

0.551415 HDAC1_TOP1_TGFB1 0.016288291 1 0.001414066 0.657327542 0.290067 0.480935 0.633316 0.4613 EGFR_HDAC1_TUBA1A 0.828180313 0.998079201 0.47921227 0.980531697 0.302806 0.633523 0.34274

0.419057 HDAC1_MAP2K1_TYMS 0.99846417 0.617525232 0.258258943 0.373917991 0.413503 0.320454 0.633592 0.45007 HDAC1_TOP1_TUBA1A 0.003926827 0.996942431 0.065824013 0.66305268 0.179768 0.636336 0.642349 0.469078 EGFR_ERBB2_TOP1 0.98453115

0.023626456 0.999032191 0.588383349 0.643012 0.253187 0.06

831 0.299922 IKBKB_TUBA1A_PIK3C3 0.97619694 0.862715

26 0.236207718 0.324710173 0.3679 −0.06753 0.651402 0.281836 DNMT1_IKBKB_TOP1 0.505410052 0.030869771 0.843907135 0.999999995 0.656228 0.502199 0.269357 0.467158 MTOR_POLA1_TYMS 0.172835786 0.998774406 0.999949461 0.99971857 0.641041 0.49756 0.658701 0.597438 HDAC1_POLA1_TOP1 0.490017845 0.237322272 0.045628483 0.045690461 0.664813 −0.09291 −0.0966 0.109085 POLA1_TOP1_TYMS 0.002154863 0.04135764 0.21830131 0.530500744 0.036432 0.665559 0.185198 0.269494 HDAC1_MTOR_POLA1 0.093842801 0.999999975 0.999988522 0.993673408 0.445345 0.681321 0.531376 0.549654 POLA1_TOP1_PIK3C3 0.06354075 0.721559784 0.235961548 0.934350514 0.303109 0.684724 0.312001 0.422813 TUBA1A_PIK3C3_TGFB1 0.69896234 0.135323833 0.985399001 0.975995927 0.688109 0.416744 0.135874 0.395321 TOP1_TUBA1A_TGFB1 0.082693874 0.405628324 0.691847211 0.2

7277692 0.59823 0.478898 0.690127 0.586715 ERBB2_TOP1_HDAC1 0.160000085 0.999996548 0.044159681 0.998843501 0.416675 0.691932 0.355669 0.481161 DNMT1_POLA1_TOP1 0.990519308 0.25522837 1 0.994425786 0.69703 0.457022 0.184163 0.430614 MTOR_TUBA1A_TGFB1 0.441809615 0.194188539 0.417940204 0.887038401 0.700591 0.560422 0.547738 0.501449 MTOR_TOP1_TUBA1A 0.000160288 0.183555398 0.562004086 0.753606311 −0.25377 0.701749 0.456998 0.227652 CDK4_ERBB2_MTOR 0.783150733 0.98129067 0.094144108 0.025951945 0.618293 0.701539 0.71282 0.677015 DNMT1_TOP1_TYMS 0.04907830

0.977188773 0.118373787 0.992

3988 0.475806 0.71378 0.351713 0.506456 HDAC1_IKBKB_TOP1 0.388150211 0.102808586 0.998986913 0.999999412 0.719561 0.412329 0.448658 0.52092 HDAC1_MTOR_PIK3C3 0.170937239 0.999915

02 0.203705978 0.426647586 0.574177 0.355159 0.722382 0.543089 CDK4_ERBB2_TOP1 0.290191177 0.112461255 0.814764388 0.999994325 0.722933 0.456998 0.26

394 0.470388 TUBA1A_TYMS_PIK3C3 0.630445587 0.998491085 0.894578927 0.866789355 0.598803 0.723721 0.089585 0.442694 EGFR_TYMS_PIK3C3 0.887429326 0.302228736 0.939797563 0.999995995 0.723849 0.486429 0.248482 0.473472 CDK4_POLA1_TGFB1 0.999977106 0.195422603 0.962507201 0.024004942 0.608312 0.352064 0.725122 0.553802 EGFR_IKBKB_TOP1 0.190879837 0.113844526 0.557668827 0.983780113 0.730224 0.559409 0.348375 0.538005 ERBB2_POLA1_TOP1 0.999691276 0.314296818 0.58715985 0.924796008 0.730339 0.219246 0.154551 0.345484 CDK4_M

OR_TUBA1A 0.487821211 0.139497818 0.

47627849 0.044658713 0.624469 0.594694 0.73101 0.549033 IKBKB_MTOR_PIK3C3 0.290015466 0.983406328 0.005209651 0.091375059 0.431181 0.177012 0.740153 0.431158 HDAC1_POLA1_PIK3C3 0.49404774 0.551618366 0.694298414 0.992710419 0.741856 0.286853 0.362058 0.450708 POLA1_TOP1_TUBA1A 0.000965426 0.566228261 0.551300117 0.999999857 −0.02441 0.760797 0.441855 0.353003 DNMT1_ERBB2_TOP1 0.488956951 0.181702937 0.856281711 0.999031462 0.772548 0.435761 0.227597 0.461881 EGFR_MTOR_TOP1 0.999906205 0.589882152 0.819986259 0.746841584 0.774704 0.512232 0.01668 0.397364 DNMT1_MAP2K1_TOP1 0.491036624 0.335044249 0.795640651 0.950130391 0.77938 0.263915 0.39111 0.462568 HDAC1_TOP1_TYMS 0.052202116 0.720691695 0.275390265 0.974706613 0.383056 0.779802 0.528133 0.555217 MTOR_

YMS_PIK3C3 0.047217787 0.999472996 0.6080471 0.070048787 0.583356 0.789012 0.310764 0.548479 MTOR_TOP1_FGF2 5.63754E−05 0.830843191 0.692047252 0.624707528 0.16167 0.800955 0.461724 0.30195 EGFR_HDAC1_TYMS 0.9592182

4 0.999991

76 0.010357503 0.110082295 0.551602 0.802048 0.531721 0.623961 EGFR_HDAC1_TOP1 0.150069278 0.433295022 0.478339031 0.885549284 0.821661 0.652396 0.405038 0.617171 MTOR_TOP1_TYMS 0.007285921 0.161524404 0.759177272 0.785833383 0.111585 0.824073 0.504852 0.450417 ERBB2_MTOR_

OP1 0.974639963 0.742993637 0.097793377 0.403404578 0.831287 0.280221 −0.02898 0.315499 IKBKB_

OP

_POLA1 0.043885788 0.650235827 0.6

1645047 0.890943841 0.237834 0.832636 0.197817 0.395435 TOP1_TUBA1A_TYMS 0.050678937 0.999984126 0.999986952 0.686609687 0.597731 0.280228 0.83

075 0.554392 DNMT1_EGFR_TOP1 0.143750163 0.545285449 0.297005605 0.443531118 0.846593 0.523002 0.501194 0.516229 POLA1_

OP1_

GFB1 0.009168961 0.94534317 0.875140097 0.99997631 0.144164 0.861281 0.491102 0.469837 TOP1_FGF2_PIK3C3 0.549151343 0.999566995 0.832038455 0.641985294 0.573764 0.2037

3 0.861446 0.522102 CDK4_POLA1_TOP1 0.768739139 0.830582756 0.998819299 0.99999884 0.865476 0.520468 0.265169 0.530988 TOP1_TUBA1A_PIK3C3 0.082335023 1 0.893197064 0.944408939 0.525332 0.067954 0.888594 0.454404 TOP1_TUBA1A_FGF2 0.000584485 0.483046742 0.999998642 0.924943825 0.321702 0.234325 0.905372 0.459677 CDK4_TOP1_MTOR 0.535515102 0.932811138 0.964574925 0.894773276 0.557484 0.906654 0.057684 0.464484 EGFR_TOP1_TYMS 0.124921844 0.995961917 0.920056605 0.889148891 0.501433 0.921144 0.399148 0.592122 MTOR_TOP1_

GFB1 0.033383026 0.99296759 0.999916337 0.999628065 0.181094 0.996446 0.772533 0.610814 MAP2K1_MTOR_TOP1 0.939755324 0.999943003 0.99999999 0.999999806 1.002694 0.722184 0.077629 0.549011 MAP2K1_POLA1_TOP1 0.423954884 0.999945543 0.855026253 0.960607887 1.005518 0.627726 0.227672 0.588413 HDAC1_MTOR_TOP1 0.843378545 0.89701173 0.999999888 0.999999873 1.219891 0.698143 0.449952 0.761516 MTOR_TOP1_PIK3C3 0.175818781 0.957324714 0.693938182 0.995941988 0.370045 1.288189 0.623438 0.720

02

indicates data missing or illegible when filed

5.4 Validation of Screen Hits with Matching Drug Combinations

Azacitidine (AZA), fludarabine (FLU), and erlotinib (ERL) were used to target DNMT1, POLA1, and EGFR, respectively. Lapatinib (LAP) was used to inhibit ERBB2, while it also acts on EGFR that belongs to the same Erb protein family. The three-drug treatment of AZA, FLU, and ERL/LAP showed significantly stronger growth-inhibitory effects than the single- and double-drug treatments (FIG. 5A-B), and also resulted in a different set of perturbed genes including those involved in cell cycle regulation when comparing cells treated with the three-drug regimen to all of the respective two-drug combinations (FIG. 10 ). Synergy among the three drugs suppressing ovarian cancer cell growth was confirmed using the DiaMOND scoring method (FIG. 5C) (Cokol et al., 2017). The fractional inhibitory concentration (FIC) scores for AZA+FLU+ERL and AZA+FLU+LAP were 0.64 and 0.8, respectively, in OVCAR8-ADR cells. By comparing the drug dose required for achieving half maximal inhibiting concentration (IC₅₀) upon single-, double- and triple-drug treatments, we found that the triple-drug formulation of AZA+FLU+ERL demand ˜4.5-fold less of each component (and ˜3.7-fold less for AZA+FLU+LAP). Similar results were observed when measuring other inhibitory concentrations (IC₃₀, IC₄₀, and IC₆₀; FIG. 11 ). The synergy among the three drugs (AZA+FLU+ERL or LAP) was also detected in OVSAHO cells (FIG. 12 ). We also confirmed the synergy among the three matching drugs (Ribociclib (RIB)+Trametinib (TRA)+FLU) for our third screen hit (i.e., CDK4+MAP2K1+POLA1) in suppressing ovarian cancer cell growth (FIG. 5D). These results indicate that our platform enables high-throughput screening and identification of synergistic three-way therapeutic combinations.

5.5 CRISPR-Cas9 Screen for Drug Pairs Against Ovarian Cancer

Via one-pot reactions using CombiGEM-CRISPR v2.0 (FIG. 6B), we built a paired gRNA library targeting 52 druggable genes (3 gRNAs per gene; Tables S2 and S3), whose expressions were shown in OVCAR8-ADR, and also other ovarian cancer cells based on the NCI-60 proteome database (Gholami et al., 2013). We selected gRNAs with on-target scores scored>0.63 (with predicted efficiency of >˜80%), except one with a score of 0.60. Three control gRNAs from the GeCKOv2 library (Shalem et al., 2014) that do not have on-target loci in the human genome were included as references. The pairwise gRNA library pool (with 159×159 gRNAs=25,281 total combinations) was then delivered into OVCAR8-ADR cells via lentiviruses. Using our established experimental pipeline (Wong et al., 2015; Wong et al., 2016), we performed Illumina HiSeq to confirm the high coverage (>99.0%) of the pairwise library and high correlation of barcode representation between the plasmid and infected cell pools (FIG. 13A-E). Using similar time windows used in our previous study, barcode abundances between day 15 and day 21 groups were compared to yield log 2 values as a measure of cell growth (FIG. 13F). Based on a selection criteria that required a mean log 2 ratios of <−1 (based on data obtained from two biological replicates with at least 50% fewer barcode counts in day 21-versus day 15-cultured cells) and multiple gRNAs targeting the same gene pair being detected with at least P<0.1, two combinations (PARP1+DNMT1 and CDK2+FKBP1A highlighted in blue and red, respectively, in FIG. 13G) were defined as top screen hits. The growth inhibition brought by these two dual-gene knockouts were validated using individual non-pooled assays, and were not resulted from the knockout of either gene (FIG. 13H; 7B).

We then evaluated the growth inhibition effects brought by these two hit combinations by treating OVCAR8-ADR cells with drug pairs. Olaparib (OLA), azacitdine (AZA), seliciclib (SEL), and sirolimus (SIR) were used as the drugs to target PARP1, DNMT1, CDK2, and FKBP1A, respectively. These drug molecules have been reported to have potent effects on their targets (McClue et al., 2002; Muvarak et al., 2016; Sabers et al., 1995; Wishart et al., 2006; Yang et al., 2017). Our results indicated that OLA and AZA act synergistically to suppress the growth of OVCAR8-ADR cells (FIGS. 13I-K) and induce G2 cell-cycle arrest (FIG. 13L), while combined treatment with SEL and SIR exerted an additive effect that renders its growth (FIGS. 13M-P). Similar growth inhibition effects were observed when these drug combinations were treated to OVSAHO and KURAMOCHI (FIG. 14 ), two other characterized cell models of HGSOC (Coscia et al., 2016; Domcke et al., 2013). Our results also corroborate with the observation that co-administration of PARP1 inhibitor talazoparib and DNMT1 inhibitor guadecitabine synergistically suppressed tumor growth in PEO1 and PEO4 cells, as well as in an OVCAR4 xenograft model (Pulliam et al., 2018), further suggesting PARP1+DNMT1 inhibitor combination as an effective therapeutic option for ovarian cancer.

5.6 CRISPR-Cas9 Screen for Drug Pairs Against Parkinson's Disease Toxicity

Our screening approach can also be applied for searching effective therapeutic combinations that enhance protection against other disease phenotypes, such as Parkinson's disease (PD)-associated toxicity. We assembled another high-coverage (99.1%) pairwise gRNA library targeting 28 druggable genes, whose ablations or matching drug inhibitors were reported to suppress neuronal toxicity (FIG. 15A-E; Table S9). The library was delivered into SK-N-MC-Cas9 cells via lentiviruses to generate dual gene knockouts, and the cells were then treated with rotenone to induce PD-associated toxicity (FIG. 15F-G). Barcode abundances between the rotenone-treated and untreated groups were compared to identify enriched gRNA combinations that protect the cells from rotenone-induced toxicity. Based on a selection criteria that required a mean log 2 fold-change of >0.378 (based on data obtained from two biological replicates with at least 30% more barcode counts in rotenone-treated versus untreated cells) and multiple gRNAs targeting the same gene pair being detected with P<0.05, our genetic screen identified HSP90B1+HDAC2 as the top hit (with six gRNA combinations identified, having an average of 51.6% increase in barcode counts) that enhances cell survival upon rotenone treatment (FIG. 15H; Table S8). The protective effect brought by the simultaneous knockout of HSP90B1+HDAC2 was validated in non-pooled assays, which was greater than that from the knockout of either gene (FIG. 15I). We further confirmed the protective effect of the matching drugs (17-(Dimethylaminoethylamino)-17-demethoxygeldanamycin (17-DMAG)+vorinostat) for this identified combination. Combined drug treatment enhanced cell survival against rotenone-induced toxicity when compared to single-drug treatments in both SK-N-MC cells (FIG. 15J) and iPSC-derived dopaminergic neurons (FIG. 15K). In addition, we observed this drug combination reduced toxicity induced by MPP+ treatment in cultured cells (FIG. 15L) and alpha-synuclein expression in transgenic flies (FIG. 15M), two other well-characterized models of PD. Our results demonstrate the versatility of our platform for screening therapeutic combinations against different disease phenotypes, including those for alleviating neurodegenerative disease phenotypes.

TABLE S8 List of pairwise gRNA combinations identified with a mean log2 ratios of >0.378 and P < 0.05 in the Parkinson disease study gRNA combination Mean log₂ FC −log₁₀ P GLIPR2sg1 + HSP90B1sg2 1.126424046 3.507991 CAPN2sg3 + PDIA3sg1 1.008682116 2.016235081 GRM5sg3 + SLC6A4sg1 0.972018541 1.776433146 RYR1sg1 + HDAC2sg2 0.955558613 2.677168034 GRM5sg1 + P4HBsg3 0.898552542 2.21645325 P4HBsg2 + CAPN5sg3 0.774513579 1.60037543 RYR1sg1 + HDAC2sg1 0.720426754 1.541352959 HDAC2sg1 + HSP90B1sg1 0.70905273 1.450972008 HSP90AA1sg3 + ROCK2sg1 0.707929211 2.30187326 SLC6A4sg2 + GRM5sg3 0.690697126 4.207515084 CAPN2sg1 + CAPN1sg2 0.676107879 1.753044643 HSP90B1sg1 + HDAC2sg3 0.675931591 1.961980123 CAPN1sg3 + CAPN5sg3 0.670296163 1.862571909 HDAC3sg3 + HDAC2sg3 0.64605226 1.383342132 P4HBsg2 + ITPR1sg1 0.644920981 1.541072995 CAPN2sg2 + CAPN1sg3 0.63840395 1.938432957 ITPR1sg1 + 5LC18A2sg1 0.636540587 1.692809095 ITPR1sg1 + PAHBsg1 0.625931199 1.362529696 HDAC3sg2 + CAPN7sg3 0.625083558 1.541140981 HDAC3sg2 + HDAC2sg2 0.618388513 2.474315139 HDAC2sg3 + HSP90B1sg1 0.615445247 1.692376051 HDAC2sg2 + SIRT2sg2 0.612752144 1.44660496 HSP90B1sg1 + HDAC2sg1 0.612133727 1.92358361 CAPN1sg1 + RPS6KA5sg2 0.595345318 2.907293971 SIRT2sg3 + RPS6KA5sg1 0.584546933 1.536953803 HDAC9sg3 + HDAC2sg3 0.583352568 2.302426443 RYR1sg2 + HDAC2sg2 0.57895447 1.705904084 HDAC3sg3 + HDAC2sg2 0.575508331 1.677065402 HDAC3sg3 + CAPN7sg1 0.562465544 1.677749106 H5P90B1sg3 + HDAC2sg1 0.561942841 1.416919338 HDAC3sg1 + RYR1sg2 0.537493278 1.426415751 CAPN5sg1 + CAPN1sg2 0.536146171 3.116720588 GRM5sg2 + P4HBsg1 0.535865982 2.481199695 HSP90B1sg1 + GLIPR2sg3 0.516928526 1.743745497 HDAC2sg3 + RYR1sg2 0.501810198 2.316441385 ITPR1sg3 + SLC18A2sg1 0.478283967 2.214358443 ITPR1sg2 + P4HBsg3 0.477238703 2.172069184 RP56KA5sg1 + CAPN1sg3 0.475250906 1.79766202 HDAC9sg1 + HDAC2sg2 0.449763451 1.375556285 RYR1sg1 + HDAC3sg2 0.447743659 1.549182472 P4HBsg1 + ITPR1sg2 0.442530566 2.115866998 HDAC2sg1 + HDAC9sg1 0.441137135 1.794058165 SIRT2sg3 + RPS6KA5sg2 0.432119816 2.161910747 H5P90B1sg3 + HDAC2sg2 0.429121726 2.456583701 RYR1sg3 + HDAC2sg1 0.429075248 2.300710139 HDAC2sg3 + HDAC9sg3 0.426839192 1.769447608 QPCTsg2 + APAF1sg3 0.422158616 1.533310963 QPCTsg3 + APAF1sg3 0.421368106 1.5030874 RYR1sg1 + HDAC3sg3 0.417220779 1.724746842 ROCK2sg2 + HSP90AA1sg1 0.412054157 1.885914996 HDAC9sg2 + HDAC2sg3 0.388977711 1.53394552 SIRT2sg1 + HDAC2sg3 0.384184713 1.303472578 CAPN2sg2 + PDIA3sg2 0.382090611 1.628332551 P4HBsg1 + CAPN5sg2 0.381402103 1.477684628

TABLE S9 List of druggable genes included in the Parkinson's disease study. Gene target Gene family Matching inhibitor drug APAF1 Apoptotic peptidase SVT016426 activating factor CAPN1 Calpain Calpastatin CAPN2 CAPN5 CAPN7 CAPN10 GLIPR2 Cysteine-rich Tat-beclin 1 peptide secretory protein GRM5 G-protein coupled MT

P receptor 3 protein GSK3B Glycogen synthase SB-216763/lithium kinase (clinically approved) HDAC1 Histone Vorinostat; Valproic deacetylase acid (clinically approved) HDAC2 HDAC3 HDAC6 HDAC9 HSP90AA1 Heat shock protein 90 17-AAG HSP90AB1 HSP90B1 ITPR1 Inositol 1,4,5- 2-APB triphosphate receptor MTOR Serine/threonine Sirolimus protein kinase PDIA1 (P4HB) Protein disulfide 16F16 isomerase PDIA3 QPC

Glutaminyl cyclase SEN170; SEN817; SN177 ROCK1 Rho-associated Y-27632; HA-1077 protein kinase ROCK2 RPS6KAS Mitogen- and stress- H89; Ro-31-8220 activated protein kinase RYR1 Ryanodine receptor Dantrolene (clinically approved) SIRT2 Sirtuin AK-7; AGK2 SLC18A2 Vesicular monoamine Tetrabenazine transporter (clinically approved) SIC6A4 Neurotransmitter Citalopram transporter (clinically approved) TGM2 Transglutaminase Cystamine

indicates data missing or illegible when filed

5.7 Discussion

In summary, we have established a CRISPR-based multi-gene knockout screening platform to address the unmet need for rapid identification of effective three-way therapeutic combinations. Via pairing drug mechanisms of action to specific genes helps accelerating the identification of effective combinations for directing secondary screens and narrows a vast number of possible combinations down to few top-performing hits for further testing. We have demonstrated that systematic characterization of three-way combinations using CRISPR-based screening discovers the rare ones with synergistic interactions as most of them showed buffering interactions and were able to validate all three screen hits with strong growth inhibition effects and three-way interactions. Our CombiGEM-CRISPR v2.0 platform has broad utility as it can also be used for identifying new two-drug regimens that inhibit cancer cell growth (FIGS. 13-14 ) and enhance protection against other disease phenotypes, such as Parkinson's disease (PD)-associated toxicity (FIG. 15 ), as well as extended to analyse interactions among >3 genetic components by using additional engineered promoters and scaffolds including our newly engineered v3.11, v.3.12, and v3.13 scaffolds (See FIG. 16 ) for multiplexed CRISPR-based editing (Reis et al., 2019).

As described in FIG. 16 , engineered gRNA scaffold variants exhibit improved on-target and low off-target activities. A, Sequence of gRNA scaffold sequences used. B, C, OVCAR8-ADR cells harboring reporter constructs with on-target (B) and off-target (C) sites were infected with lentiviruses encoding wildtype or Opti-SpCas9. The editing efficiency of the gRNA scaffold variants was measured as the percentage of cells with depleted RFP fluorescence. D, Assessment of gRNA scaffold variants for efficient on-target editing with gRNAs targeting endogenous loci. The percentage of sites with indels was measured using a T7 endonuclease I (T7E1) assay. The ratio of the on-target activity of gRNA scaffold variants to the activity of scaffold was determined, and the median and interquartile range for the normalized percentage of indel formation are shown for the 5 loci tested. Each locus was measured three times. E, GUIDE-seq genome-wide specificity profiles for the panel of gRNA scaffold variants paired with the indicated gRNAs. Mismatched positions in off-target sites are colored, and GUIDE-seq read counts were used as a measure of the cleavage efficiency at a given site.

This platform is also versatile to be used together with dCas9-based CRISPR interference systems (Qi et al., 2013) to partially lower the target gene expressions for mimicking drug inhibitor effects. This platform could be coupled with other technologies like single-cell RNA-seq to explore different cell signatures and contribute to the generation of druggable gene interaction network using existing knowledge (Adamson et al., 2016; Bassik et al., 2013; Chow et al., 2019; Du et al., 2017; Han et al., 2017; Shen et al., 2017). The platform presented in this study is easy-to-implement and will be valuable for perturbing the multi-layer genetic networks for understanding complex biological systems and designing new combination therapies.

6. EXAMPLES Experimental Model and Subject Details Cell Culture and Generation of Cell Lines

HEK293T (female) and SK-N-MC (female) cells were obtained from American Type Culture Collection (ATCC). OVCAR8-ADR (female) cells were a gift from T. Ochiya (Japanese National Cancer Center Research Institute, Japan)(Honma et al., 2008). The identity of the OVCAR8-ADR cells was confirmed by a cell line authentication test (Genetica DNA Laboratories). KURAMOCHI (female) and OVSAHO (female) cells were obtained from Japanese Collection of Research Bioresources (JCRB) Cell Bank. iPSC-derived dopaminergic neurons were obtained from TGD Life Company Limited. OVCAR8-ADR-Cas9 and SK-N-MC-Cas9 cells were generated by transducing pAWp30 (Addgene, 73857) into the OVCAR8-ADR and SK-N-MC cells, respectively, followed by selection using zeocin (Life Technologies) for stable Cas9-integrated cells. The Streptococcus pyogenes Cas9 was used in this study. OVCAR8-ADR reporter cells that stably express RFP and GFP were generated by transducing the cells with pAWp9, followed by sorting based on GFP and RFP signals. The reporter cells were then infected with pAWp30 to stably integrate Cas9 after zeocin selection. HEK 293T and S-N-MC cells were cultured in DMEM supplemented with 10% FBS and 1× antibiotic-antimycotic (Life Technologies) at 37° C. with 5% CO₂. KURAMOCHI, OVSAHO, and OVCAR8-ADR cells were cultured in RPMI 1640 supplemented with 10% FBS and 1× antibiotic-antimycotic at 37° C. with 5% CO₂. Cells were checked for mycoplasma contamination every three or four months and were never tested positive.

Methods Details Plasmid Construction

The vectors used in this study (Table S5) were generated by standard molecular cloning strategies, including PCR, oligo annealing, restriction enzyme digestion, ligation, and Gibson assembly. Custom oligonucleotides were purchased from Genewiz. Vectors were transformed into E. coli strain DH5a competent cells and selected with ampicillin (100 μg/ml, USB) or carbenicillin (50 μg/ml, Teknova). DNA was extracted and purified by Plasmid Mini (Takara and Tiangen) or Midi preparation (Qiagen) kits. Sequences of the vectors were verified with Sanger sequencing.

TABLE S5 This file contains a list of constructs used in this work Construct ID Design Reference pAWp92 pBT264-mutH1p-{2xBbsl}-sgRNA scaffold-{Mfel} This study pAWp28 pBT264-U6p-{2xBbsl}-sgRNA scaffold-{Mfel} Wong et al., PNAS, 2016; 113(9): 2544-9 pAWp100 pBT264-mutmU6p-{2xBbsl}-sgRNA scaffold-{Mfel} This study pAWp28-v1 scaffold pBT264-U6p-{2xBbsl}-v1 sgRNA scaffold-{Mfel} This study pAWp102 pBT264-mutmU6p-{2xBbsl}-v2 sgRNA scaffold-{Mfel} This study pAWp30 pFUGW-EFSp-Cas9-P2A-Zec Wong et al., PNAS, 2016; 113(9): 2544-9 pAWp40 pFUGW-EFSp-BFP-{Sbfl This study pAWp12 pFUGW-CMVp-GFF Wong et al., Nat Biotechnol, 2015; 33(9): 952-961 pAWp9 pFUGW-UBCp-RFP-CMVp-GFP-{BamHI + EcoRI} Wong et al., PNAS, 2016; 113(9): 2544-9 pAWp9-1 pFUGW-UBCp-RFP-CMVp-GFP-U6p-GFPsg1-sgRNA scaffold Wong et al., PNAS, 2016; 113(9): 2544-9 pPZp4 pFUGW-UBCp-RFP-CMVp-GFP-mutH1p-GFPsg1-sgRNA scaffold This study pPZp15 pFUGW-UBCp-RFP-CMVp-GFP-mutmU6p-GFPsg1-sgRNA scaffold This study pAWp76 pFUGW-UBCp-RFP-CMVp-GFP-U6p-GFPsg1-v1 sgRNA scaffold This study pPZp23 pFUGW-UBCp-RFP-CMVp-GFP-mutmU6p-GFPsg1-v2 sgRNA scaffold This study pAWp9-H1G1/UGR1 pFUGW-UBCp-RFP-CMVp-GFP-mutH1p-GFPsg1-sgRNA scaffold-U6p- This study RFPsg1-sgRNA scaffold pPZp58 pFUGW-EFSp-BFP-mutH1p-RFPsg1-sgRNA scaffold-U6p-GFPsg1- This study sgRNA scaffold pPZp59 pFUGW EFSp BFP mutH1p RFPsg1 sgRNA scaffold U6p GFPsg1 This study v1 sgRNA scaffold pPZp66 pFUGW-EFSp-BFP-mutH1p-RFPsg1-sgRNA scaffold-U6p-GFPsg1- This study sgRNA scaffold-mutmU6p-BFPsg3-sgRNA scaffold pPZp67 pFUGW-EFSp-BFP-mutH1p-RFPsg1-sgRNA scaffold-U6p-GFPsg1- This study v1 sgRNA scaffold-mutmU6p-BFPsg3-v2 sgRNA scaffold PZp97 pFUGW-CMVp-GFP-U6p-FKBP1Asg2-v1 sgRNA scaffold This study PZp101 pFUGW-CMVp-GFP-mutH1p-CDK2sg3-sgRNA scaffold This study PZp99 pFUGW-CMVp-GFP-U6p-DNMT1sg2-v1 sgRNA scaffold This study PZp103 pFUGW-CMVp-GFP-mutH1p-PARP1sg2-sgRNA scaffold This study pPZp104 pFUGW-CMVp-GFP-mutH1p-CDK2sg1-sgRNA scaffold-U6p- This study FKBP1Asg1-v1 sgRNA scaffold pPZp105 pFUGW-CMVp-GFP-mutH1p-CDK2sg3-sgRNA scaffold-U6p- This study FKBP1Asg2-v1 sgRNA scaffold pPZp106 pFUGW-CMVp-GFP-mutH1p-DNMT1sg3-sgRNA scaffold-U6p- This study PAPR1sg2-v1 sgRNA scaffold pPZp107 pFUGW-CMVp-GFP-mutH1p-PARP1sg2-sgRNA scaffold-U6p- This study DNMT1sg2-v1 sgRNA scaffold pPZp138-1 pFUGW-CMVp-GFP-mutH1p-PPP1R

2Csg-sgRNA scaffold- This study (Safe harbour U6p-THUMPD3-AS1sg1-v1 sgRNA scaffold-mutmU6p- loci TKO combination 1) CCR5sg-v2 sgRNA scaffold pPZp138-2 pFUGW-CMVp-GFP-mutH1p-PPP1R

2Csg-sgRNA scaffold- This study (Safe harbour U6p THUMPD3-AS1sg2-v1 sgRNA scaffold-mutmU6p-CCR5sg- loci TKO combination 2) v2 sgRNA scaffold pPZp138-3_4D pFUGW-CMVp-GFP-mutH1p-dummysg3-sgRNA scaffold-U6p- This study (Dummy control dummysg1-v1 sgRNA scaffold-mutmU6p-dummysg2-v2 gRNA combination 1) sgRNA scaffold pPZp138-3_RT pFUGW-CMVp-GFP-mutH1p-dummysg3-sgRNA scaffold-U6p- This study (Dummy control dummysg3-v1 sgRNA scaffold-mutmU6p-dummysg2-v2 gRNA combination 2) sgRNA scaffold PZp125-1 pFUGW-CMVp-GFP-mutH1p-EGFRsg2-sgRNA scaffold This study PZp200-a pFUGW-CMVp-GFP-mutH1p-POLA1sg1-sgRNA scaffold This study PZp200-c pFUGW-CMVp-GFP-mutH1p-ERBB2sg1-sgRNA scaffold This study PZp200-g pFUGW-CMVp-GFP-U6p-DNMT1sg1-sgRNA scaffold This study PZp201-g pFUGW-CMVp-GFP-mutH1p-EGFRsg2-sgRNA scaffold- This study U6p-DNMT1sg1-v1 sgRNA scaffold PZp201-j pFUGW-CMVp-GFP-mutH1p-POLA1sg1-sgRNA scaffold- This study U6p-EGFRsg2-v1 sgRNA scaffold PZp201-a pFUGW-CMVp-GFP-mutH1p-POLA1sg1-sgRNA scaffold- This study U6p-DNMT1sg1-v1 sgRNA scaffold PZp201-c pFUGW-CMVp-GFP-mutH1p-ERBB2sg1-sgRNA scaffold- This study U6p-DNMT1sg1-v1 sgRNA scaffold PZp201-i pFUGW-CMVp-GFP-mutH1p-ERBB2sg1-sgRNA scaffold- This study mutmU6p-POLA1sg1-v2 sgRNA scaffold pPZp202-c pFUGW-CMVp-GFP-mutH1p-ERBB2sg1-sgRNA scaffold- This study (DNMT1 + U6p-DNMT1sg1-v1 sgRNA scaffold-mutmU6p- POLA1 + ERBB2 TKO POLA1sg1-v2 sgRNA scaffold combination 1) pPZp202-d pFUGW-CMVp-GFP-mutH1p-ERBB2sg2-sgRNA scaffold- This study (DNMT1 + U6p-DNMT1sg2-v1 sgRNA scaffold-mutmU6p- POLA1 + ERBB2 TKO POLA1sg2-v2 sgRNA scaffold combination 2) PZp202-e pFUGW-CMVp-GFP-mutH1p-CDK4sg3-sgRNA scaffold- This study (CDK4 + U6p-MAP2K1sg1-v1 sgRNA scaffold-mutmU6p- MAP2K1 + POLA1 TKO POLA1sg1-v2 sgRNA scaffold combination 1) PZp202-f pFUGW-CMVp-GFP-mutH1p-CDK4sg3-sgRNA scaffold- This study (CDK4 + U6p-MAP2K1sg2-v1 sgRNA scaffold-mutmU6p- MAP2K1 + POLA1 TKO POLA1sg2-v2 sgRNA scaffold combination 2) pPZp202-b pFUGW-CMVp-GFP-mutH1p-DNMT1sg2-sgRNA scaffold- This study (DNMT1 + U6p-EGFRsg2-v1 sgRNA scaffold-mutmU6p- POLA1 + EGFR TKO POLA1sg2-v2 sgRNA scaffold combination 1) pPZp202-g pFUGW-CMVp-GFP-mutH1p-EGFRsg2-sgRNA scaffold- This study (DNMT1 + U6p-DNMT1sg1-v1 sgRNA scaffold-mutmU6p- POLA1 + EGFR TKO POLA1sg1-v2 sgRNA scaffold combination 2) pPZp202-h pFUGW-CMVp-GFP-mutH1p-EGFRsg1-sgRNA scaffold- This study (DNMT1 + U6p-DNMT1sg2-v1 sgRNA scaffold-mutmU6p- POLA1 + EGFR TKO POLA1sg1-v2 sgRNA scaffold combination 3) pPZp202-i pFUGW-CMVp-GFP-mutH1p-POLA1sg1-sgRNA scaffold- This study (DNMT1 + U6p-DNMT1sg1-v1 sgRNA scaffold-mutmU6p- POLA1 + EGFR TKO EGFRsg2-v2 sgRNA scaffold combination 4) pBEp33 pFUGW-CMVp-GFP-mutH1-HSP90B1sg1-sgRNA scaffold- This study U6p-HDAC2sg1-v1 sgRNA scaffold pBEp34 pFUGW-CMVp-GFP-mutH1-HDAC2sg3-sgRNA scaffold- This study U6p-HSP90B1sg1-v1 sgRNA scaffold

indicates data missing or illegible when filed

To construct storage vectors with mouse U6 (mU6)- and human H1 (hH1) promoter-gRNA WT scaffold sequences, the promoter sequences were amplified from mouse and human genomic DNAs, respectively, and cloned into the vector backbone of pAWp28 (Addgene, 73850). pAWp28 is the storage vector with human U6 (hU6) promoter-gRNA WT scaffold sequence. Storage vectors with hU6-gRNA v1 scaffold and mU6-gRNA v2 scaffold were created by PCR-based mutagenesis. To drive gRNA expression to target the gene of interest, oligo pairs with gRNA target sequences were synthesized, annealed, and cloned into BbsI-digested storage vectors by T4 DNA ligase (New England Biolabs). To generate lentiviral vectors for expression of single gRNA targeting GFP, RFP, and BFP gene, the gRNA expression cassettes were released from the storage vectors by digestion with BglII and EcoRI enzymes (Thermo Fisher Scientific) and cloned into pAWp9 vector (Addgene, 73851) using ligation via the compatible stick ends generated by digestion of the vector with BamHI and EcoRI enzymes (Thermo Fisher Scientific). To build lentiviral vectors for expression of multiple gRNAs targeting the fluorescent proteins, the second gRNA expression cassette with hU6-gRNA-v1 (or WT) scaffold was released from the storage vector by digestion with BglII and EcoRI enzymes, and ligated into the BamHI- and EcoRI-digested storage vector containing the first gRNA expression cassette with hH1-gRNA-WT scaffold. Similarly, the third gRNA expression cassette with mU6-gRNA-v2 (or WT) scaffold was released from the storage vector by digestion and ligated into the storage vector harbouring the first and second gRNA expression cassettes. Lentiviral vectors were then generated by amplifying the pairwise or three-way gRNA expression cassettes from the storage vector by PCR, and cloned into the SbfI-digested pFUGW vector backbone (pAWp40) by Gibson assembly.

Guide RNA Library Design and Assembly

The gRNAs used in this study were designed based on GPP sgRNA Designer (Table S3). For the pairwise gRNA libraries, three gRNAs were selected per target gene based on the following criteria: 1) on-target efficacy scores are >0.6; 2) off-target ranks are <100; and 3) target sites are within 5-65% of the protein-coding sequence. gRNA sequences containing BamHI, EcoRI, BglII, and MfeI digestion sites were excluded to avoid incompatibility with CombiGEM. For the three-wise combinatorial gRNA library, two gRNAs were selected per target gene using the same criteria, except that their on-target efficacy scores are all >0.64. inDelphi and FORECasT were applied to predict the frameshift rate of gRNA. The gRNA sequences were inputted into BLAST to extract the 70-nucleotide context sequences of the gRNAs. The PAM sequence index were located in the 70-nt sequences and were inputted alongside with the context sequence into inDelphi and FORECasT, which were downloaded from GitHub. The K562 cell line was the prediction model used in inDelphi, and the output frameshift scores are extracted from the “Frameshift frequency” option. The output summary file from FORECasT was inputted into a Python code calculating the predicted frameshift frequency by summing up the percentage of the target frameshift categories that are not multiples of three then dividing the sum by 10.

To assemble the gRNA libraries (FIG. 6B), oligo pairs with the gRNA target sequence, two BbsI restriction digestion sites, and a unique 8-bp barcode were annealed, pooled at an equal molar ratio, and cloned into storage vector backbones containing the hH1, hU6, and mU6 promoter sequences (pAWp92, AWp28, and pAWp100, respectively). The gRNA scaffold sequences (WT, v1, and v2) were then inserted into the vectors to create three pooled libraries of barcoded single gRNA expression cassette. The combinatorial gRNA libraries were assembled using the CombiGEM-CRISPR method (Wong et al., 2016a). The first pool of inserts was released from the storage vector containing the hH1-gRNA-WT scaffold by digestion with BglII and MfeI enzymes and ligated into the BamHI- and EcoRI-digested pAWp12 (Addgene, 72732) to generate the barcoded single gRNA library in a lentiviral vector. Then, the second pool of inserts was released from the storage vector containing the hU6-gRNA-v1 scaffold by digestion and ligated into the lentiviral vector containing the first gRNA expression cassette to generate the barcoded pairwise gRNA library. Similarly, the third pool of inserts was released from the storage vector containing the mU6-gRNA-v2 scaffold and inserted into the lentiviral vector containing the two gRNA expression cassettes to generate the barcoded three-way combinatorial gRNA library. The three-way combinatorial gRNA library was delivered into OVCAR8-ADR cells using lentiviruses, and Sanger sequencing analysis was performed on genomic DNA extracted from single cell-derived clones and confirmed the majority of assembled barcoded gRNA constructs (7 out of 8 colonies) harbored the expected gRNA target sequences. To construct the individual combinatorial gRNA vectors used in the validation experiments, the same assembly strategy was used, except that the annealed oligo pairs were not pooled.

Lentiviral Vector Generation and Transduction

The second-generation lentiviral vector system was used in this study. HEK293T cells were transfected by FuGene HD transfection reagent (Promega) according to manufacturer's instructions in 6-well plate, with 0.5 μg of pCMV-VSV-G, 1 μg of pCMV-dR8.2-dvpr, and 0.5 μg of the respective lentiviral vector per well. Lentivirus-containing supernatants were collected at 48 and 72 hrs post-transfection, which are then combined and filtered by 0.45 m polyethersulfone membrane (Pall). For routine transduction, we applied 300 μL of the filtered supernatant to one well of 12-well plate in the presence of 8 μg/ml polybrene (Sigma), with cell confluence at about 30%. For library transduction, Cas9-expressing cells were seeded onto 150-mm culture dishes at confluence about 50% with the cell number roughly equals 400-fold representation of the library size, and were transduced by the viruses at a multiplicity of infection (MOI) of ˜0.3, to ensure most cells were infected with just one virion.

Flow Cytometry, Cell Cycle Analysis, and Cell Sorting

To prepare samples for flow cytometry, cells were trypsinized and resuspended in FACS buffer (PBS with 2% FBS). BD LSR Fortessa analyser (Becton Dickinson) was used to detect the signal of TurboRFP, EGFP, and mTagBFP by 561 nm yellow-green laser (610/20 nm), 488 nm blue laser (530/30 nm), and 405 nm violet laser (450/50 nm), respectively. For cell cycle analysis, cells were fixed by ice-cold 70% ethanol at 4° C. for 1 hr, and then rehydrated by replacing the ethanol with PBS for 15 min at room temperature. To remove RNAs, RNase A (10 mg/ml) was added to the cells and incubated at 37° C. for 15 min. Genomic DNA contents were stained by propidium iodide (PI; Invitrogen) for 1 hr at room temperature in dark. Signal was detected by 561 nm yellow-green laser (586/15 nm) using a BD LSR Fortessa analyser. FlowJo software (v10.5.3, Becton Dickinson) was used for data analysis. For cell sorting, samples were prepared similarly as for FACS analysis, except that FACS buffer was supplemented with 2× antibiotic-antimycotic. BD Influx cell sorter (Becton Dickinson) equipped with 100-μm nozzle (24 psi with a frequency of 39.2 kHz) was used. GFP-positive cells were detected by 488 nm blue laser (530/40 nm) and sorted using 1.0 Drop Pure mode. For cells being infected with the screening libraries, the 1-2% cells that had the strongest GFP signals were not collected to minimize the chance of acquiring cells that were infected with more than a single virion. At least 100-fold more cells than the library size were collected.

Sample Preparation for Barcode Reading

For library-transduced cell pool, genomic DNA was extracted from cells with DNeasy Blood and Tissue kit (Qiagen) and quantified by Quant-iT PicoGreen dsDNA Assay kit (Life Technologies). To extract the 298-bp barcode-containing fragments, 0.5 ng of library plasmid DNA and 800 ng of genomic DNA per 50 μl of PCR reaction were used for PCR amplification using Kapa HiFi Hotstart Ready-mix (Kapa Biosystems). The forward and reverse primers used were 5′-GGATCCGCAACGGAATTC-3′ and 5′-GGTTGCGTCAGCAAACACAG-3′. The PCR amplification was kept at the exponential phase to minimize PCR bias. To ensure sufficient library coverage amplified from the genomic DNA, 20 and 10 PCR reactions were performed for the pairwise libraries used in studying ovarian cancer and Parkinson's disease, respectively, and 30 PCR reactions were performed for three-way combinatorial library. Illumina adapters and sequencing indices were then added to the amplicons by performing PCR using Kapa HiFi Hotstart Ready-mix. The forward and reverse primers used were 5′-CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGAT CTGGTTGCGTCAGCAAACACAG-3′ and 5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC TNNNNNNN(N₁₋₄)GGATCCGCAACGGAATTC-3′, where NNNNNNNN denotes a specific indexing barcode assigned for each experimental sample and (N₁₋₄) indicates the 1 to 4 nucleotides added to increase the diversity of the sequencing library. The final amplicons were purified by two rounds of size selection using a 1:0.5 and 1:0.95 ratio of Agencourt AMIPure XP beads (Beckman Coulter Genomics). Quantity and quality of samples were measured by real-time PCR using Kapa SYBR Fast qPCR Master Mix (Kapa Biosystems) with primer pair 5′-AATGATACGGCGACCACCGA-3′ and 5′-CAAGCAGAAGACGGCATACGA-3′, and analysed using a high-sensitivity DNA chip (Agilent) on an Agilent 2100 Bioanalyzer.

Barcode Sequencing Data Analysis

Barcode reads were processed from the sequencing data and normalized to count per million reads for comparison among samples. The normalized barcode counts for each gRNA combination in the cell pools were compared to the ones for dummy control gRNA combination within each sample to generate a log 2-transformed fold change. To improve data reliability, combinations that had a raw barcode read of <100 in the early time point samples from the ovarian cancer studies were excluded (FIGS. 4C and 13C). Combinations that had a raw barcode read of <20 in the untreated samples from the Parkinson's disease study were filtered out as there were fewer total reads (FIG. 15D). Also, only combinations that contain gRNAs targeting different genes, and had a coefficient of variation (CV) of <1 are included in the analysis (FIGS. 4E and 13E). Overall, 97.3% (22,921 out of 23,556 combinations) and 79.1% (21,172 out of 26,782 combinations) of the pairwise and three-way combinations are included, respectively, in the ovarian cancer study. 96.7% (6,878 out of 7,108 combinations) of the pairwise combinations are included in the Parkinson's disease study. In the ovarian cancer studies, gRNA combinations with log 2 fold-change of <−1 are listed in Tables S6 and S7. In the Parkinson's disease study, gRNA combinations with log₂ fold-change>0.378 (˜30% increase) and P<0.05 are listed in Table S8. To identify synergistic three-way combinations, the gRNA combinations targeting three non-redundant genes with a coefficient of variance<1 were grouped into the total of 455 unique three-gene targeting combinations. The R package DescTools was used to perform Dunnett's test, where the three-way combinations served as the control and being compared to the two-gene and single-gene targeting combinations (6 comparisons in total). To measure genetic interactions, a scoring system similar to one we previously described was applied (Wong et al., 2015). Genetic interaction (GI) scores were calculated by subtracting the expected fold change of the triple-gene knockout, which is estimated by the sum of respective double- and single-gene knockouts' fold changes, by the observed fold change of the triple-gene knockout, where a negative GI score indicates genetic synergy in this study. GI scores calculated for a given three-way combination represent the interaction between the third gene with the remaining two genes in combination. The GI₃ score for a three-way combination was calculated based on the geometric mean of the three GI scores. The potentially synergistic gene combinations were selected through the adjusted P-value threshold of <0.05 in all 6 comparisons from the Dunnett's test, a mean log₂ fold change of <−1, and GI₃ scores of <−0.2 (also with GI scores of <−0.14 in all 3 possible permutations (“A,B”+“C”, “A,C”+“B”, “B,C”+“A”) for the same three-way combination).

TABLE S6 List of three-way gRNA combinations identified with a mean log2 ratios of <−1 and P < 0.05 in the ovarian cancer study Mean CV gRNA combination log₂ FC −log₁₀ P (SD/mean FC) FGF2sg2 + TOP1sg2 + MAP2K1sg2 −8.586133715 1.638722442 0.28884582 TUBA1Asg2 + dummysg2 + PIK3C3sg1 −8.318545593 1.798812753 0.223819067 MSP2K1sg2 + TOP1sg1 + TGFB1sg2 −8.247628143 2.09832481 0.014853319 TUBA1Asg2 + HDAC1sg1 + FGF2sg2 −7.617088176 1.560047674 0.57889786 TGFB1sg1 + CDK4sg2 + MTORsg1 −7.506329527 1.951030989 0.909284488 MAP2K1sg2 + CDK4sg2 + TGFB1sg2 −7.282528199 1.367189908 0.530236177 FGF2sg2 + dummysg1 + MTORsg2 −4.52999296

1.64944678 0.405860991 DNMT1sg2 + HDAC1sg2 + POLA1sg2 −4.471675942 1.594113527 0.032914493 MTORsg2 + MAP2K1sg1 + IKBKBsg1 −4.38297198

1.741846615 0.080678119 IKBKBsg1 + DNMT1sg1 + MTORsg1 −4.22234579 1.882369135 0.607443195 DNMT1sg1 + dummysg2 + POLA1sg1 −4.210104706 1.334386848 0.302386547 CDK4sg2 + HDAC1sg2 + TOP1sg2 −4.126327227 1.700939935 0.228126634 DNMT1sg2 + TOP1sg2 + POLA1sg1 −4.083232757 1.341888879 0.446988565 TGFB1sg1 + MAP2K1sg1 + PIK3C3sg1 −4.05691955 1.53028173 0.289394822 TGFB1sg1 + TOP1sg2 + TUNA1Asg2 −4.060457824 2.121819003 0.300991307 MTORsg2 + HDAC1sg2 + IKBKBsg2 −4.000468401 1.374522884 0.290578222 DNMT1sg1 + DNMT1sg2 + POLA1sg1 −3.99829101 1.65311878 0.085513972 EGFRsg1 + CDK4sg3 + MTORsg1 −3.962571935 1.347040976 0.780903048 MTORsg2 + TOP1sg2 + ERBB2sg2 −3.95931421 1.51798875 0.189102698 DNMT1sg2 + MTORsg2 + CDK4sg3 −3.939644259 1.635219994 0.178493844 FGF2sg2 + CDK4sg3 + PIK3C3sg2 −3.904191954 1.507696134 0.180331902 MTORsg2 + MAP2K1sg2 + HDAC1sg1 −3.874058121 1.426242236 0.890103654 MTORsg2 + FGF2sg1 + POLA1sg1 −3.816599443 1.874581976 0.499137232 MTORsg1 + TOP1sg1 + TUBA1Asg2 −3.778784795 1.645567854 0.719456221 EGFRsg2 + TYMSsg1 + MTORsg2 −3.744747823 1.416856231 0.238712146 POLA1sg2 + dummysg1 + IKBKBsg2 −3.729139207 2.089931016 0.425751739 TUBA1Asg1 + MTORsg2 + POLA1sg1 −3.710533441 2.678258534 0.02666105 PIK3C3sg1 + dummysg2 + dummysg1 −3.64307161 1.347976042 0.243070961 TUBA1Asg1 + PIK3C3sg2 + MTORsg1 −3.623893443 1.849322314 0.10717869 TUBA1Asg2 + dummysg2 + PIK3C3sg2 −3.611119914 1.792096494 0.601125226 PIK3C3sg1 + MAP2K1sg2 + TYM5sg1 −3.573856194 1.618364448 0.136338683 HDAC1sg2 + TUBA1Asg1 + MTORsg2 −3.559216907 1.745836102 0.122050352 IKBKBsg1 + HDAC1sg2 + TUBA1Asg2 −3.545814911 1.317260587 0.156375858 MAP2K1sg2 + ERBB2sg2 + TOP1sg2 −3.499943741 1.339589445 0.592091632 TUBA1Asg2 + DNMT1sg1 + MTORsg1 −3.496994871 1.848392576 0.073277663 POLA1sg1 + TGFB1sg2 + TYM5sg1 −3.483142744 1.84858712 0.093561684 MTORsg1 + MTORsg2 + TOP1sg2 −3.465633952 1.33157665 0.678738694 TGFB1sg1 + EGFRsg2 + MTORsg1 −3.436457933 2.022835738 0.063741896 FGF2sg2 + MTORsg2 + PIK3C3sg1 −3.436290888 1.418656813 0.02993665 HDAC1sg2 + TOP1sg2 + PIK3C3sg1 −3.433743095 1.504263911 0.170928518 DNMT1sg2 + TOP1sg1 + MTORsg1 −3.424022301 1.539630118 0.114142351 POLA1sg1 + FGF2sg1 + MTORsg1 −3.414077906 1.491178283 0.151946815 IKBKBsg1 + TYMSsg1 + TOP1sg2 −3.408129785 1.487378156 0.3470298 FGF2sg2 + TUBA1Asg2 + dummysg1 −3.400971642 1.426426941 0.36456528 MTORsg1 + ERBB2sg2 + TUBA1Asg1 −3.396122753 1.525624137 0.627763928 POLA1sg1 + TUBA1Asg2 + FGF2sg2 −3.391577428 1.578838881 0.148706894 TUBA1Asg1 + EGFRsg2 + TOP1sg2 −3.38336612 1.339246809 0.87503004 TOP1sg2 + MTORsg2 + TYMSsg3 −3.379316888 1.313380542 0.191529787 TOP1sg2 + ERBB2sg2 + POLA1sg1 −3.350973747 1.576481935 0.646586337 IKBKBsg1 + DNMT1sg1 + TOP1sg2 −3.318334939 1.535047185 0.478686696 MTORsg2 + PIK3C3sg1 + FGF2sg2 −3.305799326 1.322541964 0.194764452 EGFRsg1 + MTORsg2 + DNMT1sg2 −3.290480075 1.51875451 0.109547599 FGF2sg3 + TOP1sg1 + EGFRsg2 −3.270595628 1.510302373 0.490260052 MTORsg2 + CDK4sg2 + PIK3C3sg2 −3.24058497 1.400373673 0.178888971 IKBKBsg1 + MTORsg2 + TOP1sg2 −3.194050725 1.893362461 0.060315429 MTORsg1 + MTORsg1 + TOP1sg2 −3.192107337 1.307205265 0.453094258 MTORsg2 + dummysg2 + ERBB2sg2 −3.178084078 1.363204094 0.046528237 TGFB1sg2 + TOP1sg2 + MTORsg1 −3.168464964 1.444624251 0.512230874 MTORsg2 + TOP1sg1 + PIK3C3sg2 −3.164354744 1.402521699 0.794807326 CDK4sg2 + TUBA1Asg2 + CDK4sg3 −3.153292804 1.53111918 0.699302413 dummysg1 + dummysg1 + MTORsg2 −3.141264918 1.385834196 0.19296769 MTORsg1 + HDAC1sg1 + CDK4sg3 −3.137267698 1.

48934511 0.782998454 dummysg2 + MTORsg2 + IKBKBsg2 −3.134180075 1.601564447 0.562775861 CDK4sg2 + EGFRsg1 + MAP2K1sg2 −3.120

53098 2.20961184 0.035475497 CDK4sg2 + TOP1sg2 + PIK3C3sg2 −3.101484651 1.850834019 0.492019299 MAP2K1sg1 + TYMSsg1 + MTORsg2 −3.084682717 1.918117985 0.003748465 MTORsg1 + TOP1sg2 + TOP1sg2 −3.081825566 1.929124317 0.387894

8 IKBKBsg2 + ERBB2sg1 + TOP1sg2 −3.071333235 1.591308774 0.590096213 CDK4sg3 + CDK4sg2 + MAP2K1sg1 −3.063705809 2.245249444 0.302073989 TOP1sg2 + PIK3C3sg2 + HDAC1sg2 −3.052281281 1.524283797 0.018317607 IKBKBsg1 + MTORsg2 + TGFB1sg1 −3.045370199 1.540932894 0.66937493 DNMT1sg1 + POLA1sg2 + TUBA1Asg2 −3.035479416 1.369115122 0.196714245 dummysg1 + TGFB1sg1 + TOP1sg2 −3.032348134 1.967994703 0.062847821 DNMT1sg1 + TGFB1sg1 + MTORsg2 −3.023226993 1.457619999 0.162799512 FGF2sg1 + dummysg2 + TOP1sg2 −2.943061949 1.

16091369 0.702241219 CDK4sg2 + TUBA1Asg2 + TUBA1Asg2 −2.937087574 2.199401537 0.028234469 CDK4sg2 + POLA1sg1 + POLA1sg1 −2.905084448 1.713256681 0.459738589 ERBB2sg1 + HDAC1sg1 + HDAC1sg1 −2.903277309 1.447294658 0.104410107 TGFB1sg2 + MAP2K1sg2 + PIK3C3sg2 −2.896123494 1.514871025 0.14060

299 MTORsg2 + PIK3C3sg1 + dummysg2 −2.881283379 1.376051543 0.684456863 FGF2sg2 + TOP1sg1 + CDK4sg3 −2.876681975

.162501313 0.185854108 TOP1sg1 + TGFB1sg2 + TGFB1sg2 −2.864527205 1.815572492 0.0032

1951 TOP1sg1 + CDK4sg2 + TYMSsg3 −2.857247136 1.958760549 0.056197169 HDAC1sg2 + IKBKBsg1 + IKBKBsg2 −2.853221014 1.792664293 0.084721646 MTORsg2 + TGFB1sg2 + TGFB1sg2 −2.844402318 1.3701871 0.747503556 EGFRsg1 + FGF2sg1 + POLA1sg1 −2.84006844 1.307529562 0.206371311 CDK4sg3 + MTORsg2 + PIK3C3sg2 −2.824777402 1.502775121 0.265856823 CDK4sg2 + POLA1sg2 + MTORsg1 −2.8035187 1.412113471 0.13701571

MTORsg2 + CDK4sg3 + DNMT1sg1 −2.800577786 1.623543564 0.012864996 TOP1sg2 + TOP1sg2 + ERBB2sg2 −2.795746505 2.641055932 0.02264271 HDAC1sg1 + TOP1sg1 + TOP1sg2 −2.786785117 1.735559228 0.098472254 EGFRsg2 + TGFB1sg1 + EGFRsg1 −2.782295178 1.318398213 0.495377788 MTORsg2 + IKBKBsg2 + TUBA1Asg1 −2.776023452 1.390702826 0.634161007 POLA1sg2 + TOP1sg2 + POLA1sg2 −2.770768148 1.419248611 0.152834143 TYMSsg3 + TOP1sg2 + POLA1sg2 −2.76970108 1.394996679 0.541472669 HDAC1sg2 + TYMSsg1 + POLA1sg1 −2.757064078 1.322738527 0.15795568 POLA1sg1 + DNMT1sg1 + TYMSsg1 −2.756806584 1.414264101 0.15757305 POLA1sg1 + FGF2sg2 + POLA1sg2 −2.748835494 1.676444082 0.08798269 IKBKBsg1 + HDAC1sg2 + MTORsg1 −2.747135998 1.616203377 0.569197907 POLA1sg2 + DNMT1sg2 + ERBB2sg2 −2.724259668 1.677591361 0.083859869 MAP2K1sg2 + TGFB1sg1 + MAP2K1sg2 −2.716724616 1.338543731 0.161646244 MTORsg1 + PIK3C3sg2 + MTORsg1 −2.715988931 2.087458

24 0.264281682 TYMSsg1 + dummysg1 + FGF2sg1 −2.714860478 1.978906998 0.317935994 TOP1sg1 + TYMSsg1 + ERBB2sg2 −2.711033132 1.502232657 0.073978628 CDK4sg2 + HDAC1sg2 + POLA1sg2 −2.706198521 1.576104288 0.06770972 ERBB2sg2 + PIK3C3sg2 + TYMSsg1 −2.702419157 1.471419829 0.635833334 IKBKBsg2 + TGFB1sg2 + TOP1sg2 −2.69379973 1.417741966 0.190178531 HDAC1sg1 + FGF2sg2 + MTORsg1 −2.693594568 2.002661796 0.063286889 POLA1sg1 + MAP2K1sg1 + TUBA1Asg1 −2.687200135 1.35213513 0.17548701 TGFB1sg2 + POLA1sg2 + PIK3C3sg2 −2.687022777 1.646193677 0.33111406 EGFRsg1 + MTORsg1 + TYMSsg3 −2.684685725 1.606492403 0.498775314 IKBKBsg2 + HDAC1sg2 + TOP1sg2 −2.683509951 1.479594412 0.14174346 HDAC1sg2 + CDK4sg2 + MAP2K1sg

−2.669353513 1.321026602 0.748134803 TGFB1sg1 + TYMSsg1 + TYMSsg3 −2.628039033 1.312546197 0.695992435 POLA1sg1 + POLA1sg2 + MTORsg2 −2.626234532 1.350570661 0.170192224 DNMT1sg1 + HDAC1sg1 + MAP2K1sg1 −2.617245143 1.86029835 0.102825967 dummysg2 + TOP1sg1 + TUBA1Asg2 −2.615412855 1.707638979 0.134982067 DNMT1sg2 + DNMT1sg1 + TOP1sg2 −2.604039983 1.394845091 0.659776572 TOP1sg2 + ERBB2sg1 + MTORsg2 −2.603886079 1.673704631 0.48184912 TGFB1sg2 + FGF2sg1 + POLA1sg2 −2.592913203 1.748747718 0.415257498 PIK3C3sg1 + EGFRsg1 + TOP1sg2 −2.592620176 1.310491777 0.187444102 TUBA1Asg2 + ERBB2sg2 + FGF2sg1 −2.58767017 1.478723062 0.615029833 POLA1sg1 + dummysg2 + PIK3C3sg2 −2.585099905 1.490352532 0.123749771 EGFRsg2 + POLA1sg1 + CDK4sg2 −2.579007324 1.577019222 0.101559287 EGFRsg1 + POLA1sg1 + MTORsg2 −2.578497016 1.57033641 0.375808523 FGF2sg1 + EGFRsg1 + HDAC1sg2 −2.576719022 2.158770469 0.027181043 POLA1sg1 + TOP1sg2 + TYMSsg1 −2.575747457 1.32084685 0.177602454 MAP2K1sg1 + PIK3C3sg2 + TUBA1Asg2 −2.57562504 2.306033727 0.152991097 POLA1sg2 + HDAC1sg2 + dummysg1 −2.574110395 2.626550646 0.110314712 CDK4sg2 + MTORsg1 + EGFRsg1 −2.568208926 1.403365741 0.157417873 ERBB2sg1 + ERBB2sg2 + MTORsg2 −2.567238309 2.466731582 0.020509879 TOP1sg2 + TYMSsg1 + TOP1sg2 −2.563302561 1.4

2094143 0.428140759 MTORsg2 + IKBKBsg2 + TGFB1sg1 −2.558421376 1.787155457 0.045938279 IKBKBsg2 + IKBKBsg1 + MTORsg2 −2.556641384 1.931764152 0.030593422 MAP2K1sg1 + TGFB1sg1 + FGF2sg2 −2.546794793 1.57393078 0.506049015 MTORsg2 + TGFB1sg2 + HDAC1sg1 −2.540089133 1.383650591 0.152207747 PIK3C3sg2 + MTORsg2 + FGF2sg2 −2.539873644 2.006387 0.226839939 TYMSsg1 + FGF2sg2 + FGF2sg2 −2.538858708 1.405818928 0.147500188 dummysg1 + EGFRsg2 + TYMSsg1 −2.536514427 1.551324762 0.063014821 FGF2sg2 + HDAC1sg2 + TOP1sg2 −2.530367129 1.509533257 0.551434523 POLA1sg2 + TOP1sg1 + PIK3C3sg1 −2.524467143 1.895656221 0.062034295 TGFB1sg1 + POLA1sg1 + MTORsg2 −2.517871646 1.325699488 0.092944404 TGFB1sg1 + FGF2sg1 + TOP1sg1 −2.513763238 1.366727612 0.545782956 DNMT1sg1 + ERBB2sg1 + EGFRsg1 −2.509407619 2.224676182 0.035904783 MAP2K1sg2 + CDK4sg2 + EGFRsg2 −2.502885327 1.50518527 0.00648844 dummysg2 + ERBB2sg2 + TOP1sg2 −2.502860437 1.732029148 0.183022405 DNMT1sg2 + TOP1sg1 + TUBA1Asg1 −2.497057448 1.350277802 0.686689992 DNMT1sg2 + MTORsg1 + FGF2sg2 −2.486205971 1.728965828 0.038884108 MTORsg2 + dummysg2 + TUBA1Asg2 −2.485844558 1.346369746 0.445615625 MAP2K1sg1 + MTORsg1 + DNMT1sg1 −2.476116982 1.440450237 0.561757962 TUBA1Asg2 + TUBA1Asg1 + TGFB1sg2 −2.470744843 1.527069948 0.202634371 MTORsg1 + MAP2K1sg1 + POLA1sg1 −2.455149858 1.498838729 0.122121012 MTORsg2 + POLA1sg2 + PIK3C3sg1 −2.45213818 2.018832207 0.317623119 dummysg2 + FGF2sg1 + TUBA1Asg2 −2.449780862 1.74276158 0.0823620

PIK3C3sg1 + PIK3C3sg2 + DNMT1sg2 −2.445481059 1.309996608 0.063576173 dummysg1 + TYMSsg1 + MTORsg1 −2.440383384 1.573485108 0.311475113 ERBB2sg1 + ERBB2sg1 + TOP1sg2 −2.437512267 1.448261758 0.135092281 dummysg2 + POLA1sg1 + TUBA1Asg2 −2.43712086 2.071856969 0.031787102 CDK4sg2 + TYMSsg1 + POLA1sg2 −2.435920312 1.635740711 0.367699246 POLA1sg2 + ERBB2sg2 + TOP1sg2 −2.434514792 1.302417934 0.605351054 dummysg2 + FGF2sg2 + TOP1sg2 −2.434403166 2.022383806 0.004784393 dummysg1 + EGFRsg2 + PIK3C3sg2 −2.431240801 1.301452538 0.454285547 TYMSsg1 + TGFB1sg2 + DNMT1sg2 −2.431151341 1.450099263 0.12706266 PIK3C3sg2 + TUBA1Asg2 + dummysg2 −2.430505852 2.137734919 0.229325918 HDAC1sg2 + TGFB1sg1 + TOP1sg2 −2.429966394 1.379053067 0.061700747 dummysg1 + MTORsg2 + ERBB2sg2 −2.426455402 1.387838066 0.060649523 MTORsg2 + TUBA1Asg1 + dummysg2 −2.425233326 1.577639994 0.420132802 TOP1sg2 + FGF2sg1 + MTORsg1 −2.41163662 2.084330206 0.048196978 MAP2K1sg1 + MTORsg2 + HDAC1sg2 −2.404966624 1.87614967 0.049607855 MTORsg1 + IKBKBsg2 + dummysg1 −2.402089272 1.655609911 0.084034183 CDK4sg2 + FGF2sg1 + TOP1sg2 −2.393182346 2.30607933 0.147268062 EGFRsg1 + TUBA1Asg2 + TGFB1sg2 −2.391575986 1.302588837 0.686125601 POLA1sg1 + PIK3C3sg1 + TYMSsg3 −2.384459767 1.617754505 0.261546768 TOP1sg2 + CDK4sg3 + TUBA1Asg2 −2.380917348 1.463190091 0.579124297 MTORsg1 + TYMSsg3 + PIK3C3sg1 −2.372979762 1.872116535 0.068039637 TYMSsg3 + MAP2K1sg2 + TOP1sg2 −2.371965449 1.377608906 0.151541401 ERBB2sg2 + MTORsg2 + dummysg2 −2.371035079 1.544789994 1.109106589 EGFRsg1 + TGFB1sg2 + MTORsg2 −2.365559147 1.365210683 0.14

723519 TGFB1sg2 + PIK3C3sg1 + POLA1sg1 −2.357219219 1.612127409 0.06347323 DNMT1sg1 + POLA1sg2 + PIK3C3sg2 −2.34760868 1.968304119 0.288332767 TOP1sg1 + MAP2K1sg1 + EGFRsg1 −2.345815361 1.791043297 0.07199388 MTORsg2 + HDAC1sg2 + TYMSsg3 −2.342596049 1.618443483 0.226148354 HDAC1sg2 + CDK4sg3 + ERBB2sg2 −2.340089578 1.448677083 0.12803559 IKBKBsg1 + POLA1sg2 + ERBB2sg1 −2.338087969 1.900442918 0.357504715 MAP2K1sg1 + MAP2K1sg1 + MTORsg1 −2.330100556 1.836449388 0.290578222 TUBA1Asg2 + HDAC1sg2 + DNMT1sg2 −2.323708964 1.694582743 0.070448478 dummysg2 + TYMSsg1 + POLA1sg2 −2.320295978 1.326389843 0.660627348 POLA1sg2 + MTORsg1 + PIK3C3sg1 −2.314840265 3.285765704 0.002562504 ERBB2sg2 + TOP1sg2 + TUBA1Asg1 −2.311474916 1.759607499 0.022512867 HDAC1sg1 + TOP1sg1 + PIK3C3sg1 −2.302409447 1.412595698 0.453611908 POLA1sg2 + TYMSsg3 + FGF2sg2 −2.300443655 1.646517272 0.105567925 FGF2sg1 + POLA1sg2 + TOP1sg2 −2.298784565 1.679939932 0.122769859 FGF2sg2 + TOP1sg1 + TOP1sg2 −2.288069903 2.196344476 0.034633722 TOP1sg2 + MAP2K1sg1 + TUBA1Asg2 −2.28575121 1.491104086 0.114299046 TGFB1sg2 + POLA1sg2 + TYMSsg1 −2.28229912 1.507804106 0.458264793 EGFRsg1 + POLA1sg1 + EGFRsg2 −2.268456864 2.018963655 0.230807933 MTORsg2 + DNMTsg1 + TYMSsg1 −2.26819872 1.785270768 0.073192234 TYMSsg3 + CDK4sg3 + POLA1sg1 −2.265901806 1.58507447 0.275328853 MTORsg1 + HDAC1sg2 + IKBKBsg2 −2.259177094 1.739502316 0.061123529 HDAC1sg2 + TOP1sg2 + TOP1sg2 −2.25224156 2.537912364 0.017417956 ERBB2sg2 + IKBKBsg1 + MAP2K1sg1 −2.243394998 1.42032898 0.129997172 PIK3C3sg2 + CDK4sg3 + TUBA1Asg2 −2.237565799 1.484488562 0.100968119 MTORsg2 + DNMT1sg

 + TGFB1sg2 −2.235361163 1.822731362 0.064191268 MAP2K1sg1 + TOP1sg2 + POLA1sg1 −2.234981834 1.380782569 0.047894718 TOP1sg2 + CDK4sg3 + MAP2K1sg2 −2.232467173 1.348033953 0.592811504 ERBB2sg2 + HDAC1sg2 + TYMSsg3 −2.223721455 1.312210264 0.324346931 MTORsg2 + CDK4sg3 + TYMSsg1 −2.210521278 1.945035824 0.038769931 POLA1sg2 + EGFRsg2 + TYMSsg3 −2.209450162 1.450640942 0.258637934 DNMT1sg2 + MTORsg2 + EGFRsg2 −2.205801161 1.320933096 0.153270608 TOP1sg1 + HDAC1sg1 + TGFB1sg2 −2.193919452 1.910140837 0.153681775 POLA1sg1 + TYMSsg3 + POLA1sg1 −2.193118169 1.6915254 0.03757405 MTORsg1 + MAP2K1sg2 + CDK4sg2 −2.192830581 1.4

7357516 0.043310869 HDAC1sg2 + dummysg2 + MTORsg1 −2.190934466 1.477319296 0.0870889

CDK4sg2 + MTORsg1 + dummysg1 −2.188147787 1.715094893 0.06444369 IKBKBsg2 + EGFRsg2 + TOP1sg2 −2.179624458 1.301145329 0.594835109 TYMSsg1 + TGFB1sg1 + IKBKBsg2 −2.177644894 2.873200996 0.002813975 TUBA1Asg1 + FGF2sg2 + TOP1sg2 −2.176677473 1.452523822 0.3573001 TUBA1Asg2 + EGFRsg1 + FGF2sg2 −2.176219889 1.451990014 0.389267329 FGF2sg1 + IKBKBsg1 + TOP1sg1 −2.174544392 1.317781246 0.621418641 FGF2sg2 + PIK3C3sg2 + TUBA1Asg2 −2.174521811 1.30750755 0.123264787 CDK4sg2 + dummysg1 + ERBB2sg2 −2.172533815 1.539471029 0.143254159 ERBB2sg2 + TYMSsg3 + POLA1sg1 −2.170501898 1.324869642 0.584233317 dummysg2 + PIK3C3sg2 + MTORsg2 −2.169626848 1.605981503 0.082862991 PIK3C3sg2 + TYMSsg1 + DNMT1sg2 −2.165762359 1.412323919 0.004013166 TUBA1Asg1 + TOP1sg1 + MTORsg1 −2.158695132 1.433470874 0.088549853 TGFB1sg2 + HDAC1sg1 + FGF2sg1 −2.15736068 2.31657142 0.155749521 EGFRsg1 + IKBKBsg1 + DNMT1sg2 −2.157113243 1.332008984 0.084283675 POLA1sg2 + IKBKBsg1 + EGFRsg2 −2.15484758 1.799877434 0.004772327 MTORsg2 + TYMSsg3 + IKBKBsg1 −2.153045959 2.51166289 0.159534809 PIK3C3sg2 + POLA1sg2 + MTORsg2 −2.151230455 1.935576189 0.233758933 POLA1sg2 + TOP1sg2 + MAP2K1sg1 −2.146756652 1.528165162 0.3564

2324 POLA1sg1 + DNMT1sg2 + ERBB2sg2 −2.135252635 1.650026244 0.0826439 FGF2sg2 + POLA1sg2 + PIK3C3sg2 −2.131675412 1.828144303 0.318627604 TOP1sg2 + EGFRsg1 + FGF2sg1 −2.124603105 1.903568529 0.029797357 EGFRsg2 + TOP1sg1 + CDK4sg3 −2.116290615 1.627312466 0.161785018 TOP1sg1 + MTORsg2 + IKBKBsg2 −2.115204276 1.449866769 0.53899122 DNMT1sg2 + HDAC1sg1 + TOP1sg2 −2.113674189 1.394648138 0.088698776 TOP1sg1 + MAP2K1sg1 + TUBA1Asg2 −2.108161535 1.495070588 0.10226317 DNMT1sg2 + POLA1sg1 + MAP2K1sg2 −2.108126862 1.861572009 0.061236445 TYMSsg1 + TGFB1sg2 + TGFB1sg1 −2.10329943 2.0

0024895 0.036178811 MAP2K1sg2 + MAP2K1sg1 + PIK3C3sg2 −2.101694755 1.366685169 0.105850215 MAP2K1sg2 + IKBKBsg2 + TYMSsg1 −2.10162092 1.406189539 0.508109532 TGFB1sg2 + POLA1sg1 + MAP2K1sg2 −2.101314318 1.748668919 0.069708275 TOP1sg2 + MTORsg1 + MAP2K1sg2 −2.101236878 2.14232203 0.099820397 IKBKBsg2 + TOP1sg2 + PIK3C3sg2 −2.099059928 1.32091546 0.145003611 POLA1sg1 + ERBB2sg1 + FGF2sg2 −2.097668624 2.654611981 0.007396456 MAP2K1sg1 + TYMSsg1 + IKBKBsg2 −2.09634475 1.559136446 0.088681391 MTORsg2 + FGF2sg1 + TUBA1Asg1 −2.095524984 2.116159269 0.04048096 POLA1sg2 + EGFRsg2 + CDK4sg2 −2.094326937 2.015262401 0.031312942 FGF2sg2 + TYMSsg3 + IKBKBsg1 −2.094321834 1.761106617 0.053224143 TUBA1Asg2 + TUBA1Asg2 + MAP2K1sg1 −2.092921805 1.502232455 0.066724958 IKBKBsg1 + FGF2sg2 + TUBA1Asg2 −2.090637673 1.838472331 0.036704014 TYMSsg3 + dummysg2 + POLA1sg2 −2.090531584 1.809307077 0.285148035 TOP1sg2 + EGFRsg2 + MAP2K1sg2 −2.083484109 1.520030626 0.081488565 TOP1sg1 + DNMTsg2 + CDK4sg2 −2.075663581 1.996574492 0.024108637 TGFB1sg2 + EGFRsg1 + PIK3C3sg2 −2.067737339 1.648684595 0.407045603 DNMT1sg1 + ERBB2sg1 + MTORsg2 −2.066841876 1.509974177 0.03661078 TUBA1Asg1 + POLA1sg1 + PIK3C3sg2 −2.063535357 1.438948156 0.117097487 TYMSsg1 + DNMT1sg2 + TOP1sg2 −2.061005111 1.653345253 0.358783666 EGFRsg1 + IKBKBsg2 + MAP2K1sg1 −2.053336643 1.799190389 0.284204639 CDK4sg2 + DNMT1sg1 + TOP1sg2 −2.048624388 1.428752833 0.289951877 MAP2K1sg1 + dummysg2 + POLA1sg1 −2.046791096 1.536870545 0.087102079 PIK3C3sg1 + MAP2K1sg2 + FGF2sg1 −2.043813536 1.532650494 0.455110988 MAP2K1sg1 + POLA1sg1 + EGFRsg1 −2.042079557 1.319657817 0.017771884 IKBKBsg1 + POLA1sg2 + POLA1sg1 −2.033132042 1.35899790

0.129651032 EGFRsg2 + TUBA1Asg2 + EGFRsg1 −2.0287316 1.963640221 0.256141862 TUBA1Asg2 + TOP1sg1 + MAP2K1sg2 −2.027975085 2.235620173 0.133811364 HDAC1sg2 + HDAC1sg2 + DNMT1sg1 −2.027938635 2.000152775 0.158110234 DNMT1sg1 + PIK3C3sg1 + POLA1sg2 −2.0272889 1.562370552 0.259988879 TOP1sg2 + ERBB2sg1 + HDAC1sg2 −2.026393507 1.485512755 0.46427762 POLA1sg2 + TGFB1sg2 + dummysg2 −2.026371816 1.396627761 0.329386481 TOP1sg2 + MTORsg2 + DNMT1sg1 −2.025923675 1.717743178 0.091813947 EGFRsg1 + TUBA1Asg2 + TGFB1sg1 −2.022712001 1.84521293 0.046196222 IKBKBsg2 + DNMT1sg1 + POLA1sg2 −2.021413748 1.335891495 0.12308247 MTORsg1 + FGF2sg2 + CDK4sg3 −2.020033564 1.628924533 0.078932711 FGF2sg1 + FGF2sg1 + IKBKBsg2 −2.015326779 1.730062985 0.060439044 POLA1sg2 + TOP1sg1 + FGF2sg1 −2.008440366 2.368144438 0.181782742 PIK3C3sg2 + ERBB2sg2 + POLA1sg2 −2.004584545 1.868196571 0.20702997 PIK3C3sg2 + MTORsg1 + HDAC1sg1 −1.999138816 1.534807626 0.165645743 TGFB1sg1 + HDAC1sg1 + IKBKBsg2 −1.995111933 1.329127539 0.274991507 dummysg1 + DNMT1sg2 + EGFRsg2 −1.994242919 1.395348932 0.002223503 HDAC1sg2 + PIK3C3sg2 + TUBA1Asg1 −1.989193204 2.244734416 0.000401245 IKBKBsg1 + FGF2sg1 + POLA1sg1 −1.988747131 1.847032349 0.044995857 DNMT1sg1 + DNMT1sg1 + PIK3C3sg2 −1.988414202 1.521850247 0.258625375 PIK3C3sg1 + TUBA1Asg2 + TYMSsg3 −1.979466085 1.778053854 0.324733288 PIK3C3sg2 + HDAC1sg2 + MTORsg2 −1.979068212 1.719995011 0.092419313 MAP2K1sg2 + FGF2sg2 + TYMSsg1 −1.975660839 1.437304062 0.340374483 CDK4sg2 + TUBA1Asg2 + TYMSsg1 −1.974908507 2.392079519 0.112030636 POLA1sg1 + TGFB1sg2 + TUBA1Asg2 −1.973928861 1.495301151 0.476611237 TOP1sg2 + ERBB2sg2 + FGF2sg1 −1.970861711 1.311428462 0.111882609 TOP1sg2 + TUBA1Asg2 + FGF2sg2 −1.970033314 2.324468611 0.02343994 IKBKBsg1 + FGF2sg1 + MTORsg2 −1.965920542 2.215720257 0.015649451 MAP2K1sg2 + CDK4sg3 + TYMSsg3 −1.965786148 1.532903367 0.143542099 HDAC1sg2 + TYMSsg1 + IKBKBsg1 −1.964848068 1.517839957 0.072771751 POLA1sg1 + PIK3C3sg2 + IKBKBsg1 −1.961229009 2.050431577 0.042483789 TOP1sg2 + TYMSsg3 + TYMSsg1 −1.951680284 3.933320537 0.028653827 DNMT1sg1 + MTORsg2 + TYMSsg1 −1.950739173 1.768931168 0.197205638 TOP1sg2 + POLA1sg2 + TUBA1Asg1 −1.949147107 1.440885447 0.10282645 PIK3C3sg1 + MTORsg1 + TYMSsg3 −1.948586815 1.491048987 0.097203621 MAP2K1sg2 + MTORsg2 + IKBKBsg1 −1.947364276 1.451637216 0.465744468 dummysg2 + FGF2sg1 + TOP1sg2 −1.945580108 2.45738893 0.092099775 CDK4sg3 + DNMT1sg2 + TOP1sg2 −1.940175555 1.306300768 0.189267563 TOP1sg2 + MTORsg1 + TUBA1Asg2 −1.932979042 1.561295 0.437558538 MAP2K1sg2 + TOP1sg2 + POLA1sg2 −1.931136639 1.728371019 0.250275441 IKBKBsg2 + IKBKBsg2 + TOP1sg1 −1.928036028 1.397015294 0.044768998 IKBKBsg2 + TUBA1Asg1 + TYMSsg3 −1.927623312 1.432793991 0.402346731 MTORsg1 + TOP1sg2 + PIK3C3sg2 −1.921350573 2.395472383 0.109052518 PIK3C3sg2 + MTORsg1 + DNMT1sg2 −1.919081984 1.343005312 0.140297802 MTORsg1 + TYMSsg1 + CDK4sg2 −1.919026847 2.785809701 0.062696214 FGF2sg2 + MTORsg2 + CDK4sg3 −1.918734836 1.30329142 0.156745502 FGF2sg2 + EGFRsg1 + dummysg1 −1.918422091 1.322353578 0.136082898 MAP2K1sg2 + DNMT1sg1 + TYMSsg1 −1.917007274 1.450950295 0.068603633 FGF2sg2 + TYMSsg3 + POLA1sg1 −1.91241878 2.261127852 0.142282088 MTORsg2 + CDK4sg2 + IKBKBsg2 −1.908460013

.309129902 0.137250585 FGF2sg2 + TGFB1sg2 + IKBKBsg1 −1.908040992 1.408036763 0.102030151 EGFRsg2 + DNMT1sg1 + POLA1sg1 −1.904617492 1.34504979 0.384964793 HDAC1sg1 + dummysg1 + TUBA1Asg2 −1.904167747 1.478925935 0.452430521 TOP1sg1 + MAP2K1sg1 + ERBB2sg2 −1.899744485 1.537573005 0.084283991 PIK3C3sg1 + POLA1sg2 + FGF2sg1 −1.898897026 2.177593882 0.041239503 POLA1sg2 + MAP2K1sg2 + DNMT1sg2 −1.898855776 1.323424487 0.197922185 TOP1sg2 + MAP2K1sg2 + HDAC1sg2 −1.896826771 1.80684469 0.015812236 dummysg1 + TYMSsg3 + TOP1sg1 −1.893767502 1.335526517 0.196715537 MTORsg1 + TGFB1sg2 + DNMT1sg1 −1.893371984 2.035696006 0.138488121 IKBKBsg2 + MTORsg1 + HDAC1sg1 −1.892250336 1.450671205 0.00506034 PIK3C3sg2 + TYMSsg3 + MTORsg1 −1.884056381 2.487068584 0.020659583 POLA1sg2 + MTORsg2 + dummysg1 −1.878670966 1.741973329 0.01086339 PIK3C3sg2 + TUBA1Asg2 + dummysg1 −1.867140778 1.483665415 0.096428469 TOP1sg1 + MTORsg2 + dummysg1 −1.865691114 1.526498906 0.084922004 TYMSsg3 + TOP1sg2 + EGFRsg1 −1.865505625 1.309340626 0.322292461 POLA1sg2 + PIK3C3sg2 + MTORsg2 −1.862013574 1.723908382 0.04164718 CDK4sg2 + TUBA1Asg2 + PIK3C3sg1 −1.860595445 1.465556902 0.134666407 EGFRsg1 + MAP2K1sg2 + TUBA1Asg2 −1.857528758 1.486794033 0.082634546 PIK3C3sg2 + DNMT1sg2 + TOP1sg2 −1.856917042 1.573113786 0.350705541 TYMSsg1 + HDAC1sg2 + HDAC1sg1 −1.852032988 1.990707154 0.119574568 MAP2K1sg1 + MTORsg1 + PIK3C3sg2 −1.849636767 1.93629073 0.083862896 FGF2sg2 + TGFB1sg1 + TYMSsg3 −1.849280115 1.624533901 0.067592761 EGFRsg2 + ERBB2sg2 + PIK3C3sg2 −1.846218358 1.811185497 0.042162541 FGF2sg1 + TGFB1sg2 + PIK3C3sg2 −1.845720555 2.21992383 0.16135144 DNMT1sg2 + TUBA1Asg2 + MAP2K1sg2 −1.845367624 1.930602227 0.248308652 MTORsg1 + CDK4sg3 + PIK3C3sg1 −1.845107012 2.282741679 0.00

523386 TOP1sg2 + IKBKBsg2 + TGFB1sg2 −1.843801127 1.533160043 0.389596251 MTORsg2 + TUBA1Asg2 + PIK3C3sg1 −1.84045759 1.55098509 0.087394077 CDK4sg3 + PIK3C3sg2 + POLA1sg1 −1.840014794 1.332674051 0.376282634 IKBKBsg1 + POLA1sg2 + MTORsg1 −1.839818666 1.311747725 0.019257028 dummysg2 + ERBB2sg1 + TOP1sg2 −1.839397752 1.75713807 0.002371357 TOP1sg2 + PIK3C3sg1 + MTORsg2 −1.83830925 1.401379863 0.36864189 DNMT1sg1 + dummysg2 + EGFRsg2 −1.837406687 1.484425521 0.097061087 EGFRsg1 + TUBA1Asg2 + EGFRsg2 −1.83231887

1.529201397 0.087095236 POLA1sg2 + POLA1sg1 + TGFB1sg1 −1.818992672 1.755364746 0.043361605 POLA1sg2 + IKBKBsg2 + TYMSsg1 −1.814111106 1.454004624 0.45475096 ERBB2sg1 + TYMSsg1 + EGFRsg1 −1.812895426 1.390755361 0.176434095 EGFRsg1 + TUBA1Asg2 + dummysg2 −1.810483985 2.252403906 0.18736693 MAP2K1sg2 + TGFB1sg1 + IKBKBsg1 −1.808256145 1.485815084 0.427174207 EGFRsg2 + POLA1sg2 + CDK4sg2 −1.807508205 1.55778152 0.076887512 MAP2K1sg2 + TUBA1Asg1 + DNMT1sg2 −1.805937877 1.353412431 0.439774109 CDK4sg2 + MTORsg2 + FGF2sg1 −1.80347587 1.365227137 0.503179857 dummysg1 + IKBKBsg1 + POLA1sg1 −1.802565748 1.541668034 0.3638521 dummysg1 + IKBKBsg2 + TYMSsg3 −1.8024139 1.4

4184931 0.446929166 EGFRsg1 + MAP2K1sg2 + HDAC1sg2 −1.797788815 1.346159898 0.119342308 CDK4sg3 + IKBKBsg2 + POLA1sg1 −1.79638234 1.638757577 0.074090687 DNMT1sg1 + TUBA1Asg1 + MTORsg1 −1.796315471 1.92604448 0.068457521 FGF2sg2 + IKBKBsg1 + TUBA1Asg2 −1.794649226 1.385531555 0.313875074 ERBB2sg1 + EGFRsg1 + EGFRsg2 −1.787471808 1.343933398 0.170392724 DNMT1sg1 + DNMT1sg1 + POLA1sg2 −1.786802907 1.523576253 0.225663747 IKBKBsg1 + POLA1sg1 + EGFRsg2 −1.786027569 1.772294272 0.049429492 MTORsg2 + IKBKBsg1 + HDAC1sg1 −1.785568625 2.006578495 0.092605414 PIK3C3sg2 + TUBA1Asg1 + POLA1sg2 −1.783854212 2.141788367 0.138883916 HDAC1sg1 + IKBKBsg2 + FGF2sg2 −1.782512812 1.636771828 0.001373233 POLA1sg2 + MAP2K1sg1 + ERBB2sg1 −1.779996381 1.998574019 0.041873971 MAP2K1sg2 + TYMSsg3 + TOP1sg2 −1.776088018 1.535036077 0.305124392 TUBA1Asg2 + DNMT1sg2 + dummysg1 −1.774106171 1.369501939 0.455942032 FGF2sg2 + CDK4sg2 + HDAC1sg2 −1.773921002 1.399221582 0.102187221 POLA1sg2 + TUBA1Asg1 + HDAC1sg2 −1.773505604 1.467238422 0.214515282 MAP2K1sg2 + IKBKBsg1 + MTORsg2 −1.771614067 1.440453371 0.34688377 PIK3C3sg1 + POLA2sg2 + ERBB2sg2 −1.763096153 1.662177099 0.062789408 ERBB2sg2 + TUBA1Asg2 + FDF2sg1 −1.76267477 1.317021439 0.126433939 PIK3C3sg2 + DNMT1sg1 + MTORsg1 −1.762264164 2.13739173 0.184766415 PIK3C3sg1 + TOP1sg2 + TOP1sg2 −1.762083164 1.681598967 0.061813014 TGFB1sg2 + MTORsg2 + HDAC1sg2 −1.761653173 3.078886552 0.003112009 dummysg1 + TYMSsg3 + TUBA1Asg2 −1.757607202 1.40360898 0.411093949 MTORsg2 + EDGRsg1 + IKBKBsg2 −1.752273708 2.084700151 0.219842635 TUBA1Asg1 + POLA1sg2 + EGFRsg2 −1.752038241 2.036680707 0.180455921 PIK3C3sg1 + HDAC1sg2 + TUBA1Asg2 −1.747113152 1.666180286 0.066898139 DNMT1sg2 + ERBB2sg1 + TUBA1Asg1 −1.745692895 1.851756852 0.194966291 IKBKBsg1 + CDK4sg3 + TOP1sg

−1.739813713 1.523167596 0.083281581 POLA1sg1 + FGF2sg2 + POLA1sg1 −1.738

04024 1.347407011 0.466843093 MAP2K1sg2 + PIK3C3sg1 + EGFRsg2 −1.737987597 1.412736197 0.05767105

DNMT1sg2 + EGFRsg1 + HDAC1sg2 −1.736662272 1.431025533 0.101671794 CDK4sg3 + MTORsg2 + FGF2sg2 −1.733775457 1.788267518 0.05550525 CDK4sg3 + TGFB1sg2 + TOP1sg2 −1.731746028 1.503726078 0.07

217766 EGFRsg1 + IKBKBsg1 + ERBB2sg1 −1.731654839 1.445955801 0.438059719 FGF2sg2 + EGFRsg1 + TUBA1Asg2 −1.727912714 1.627803478 0.054553686 EGFRsg2 + MTORsg2 + PIK3C3sg2 −1.722566558 1.314961686 0.478056699 TYMSsg3 + EGFRsg2 + TUBA1Asg2 −1.718311055 1.951851905 0.042896498 TOP1sg2 + CDK4sg2 + FGF2sg2 −1.717000464 1.644264764 0.018772853 ERBB2sg2 + TOP1sg1 + TYMSsg3 −1.715677992 1.460876067 0.087

82705 FGF2sg2 + TGFB1sg2 + TYMSsg1 −1.711991638 1.637030027 0.060124915 HDAC1sg1 + PIK3C3sg2 + MTORsg2 −1.711079527 1.40619428 0.311567769 PIK3C3sg2 + MTORsg2 + MAP2K1sg2 −1.708766199 1.64222607 0.028369019 HDAC1sg1 + MTORsg2 + EGFRsg

−1.708367574 1.821084463 0.178469923 POLA1sg1 + MAP2K1sg1 + CDK4sg3 −1.707795617 1.538915405 0.080133074 TOP1sg2 + PIK3C3sg1 + ERBB2sg2 −1.702022446 1.922150023 0.144523725 MTORsg1 + ERBB2sg1 + HDAC1sg2 −1.700757874 2.471148416 0.081897221 ERBB2sg1 + TOP1sg2 + TYMSsg3 −1.700623589 1.461714514 0.235817498 ERBB2sg2 + POLA1sg1 + TYMSsg3 −1.699661632 1.540052297 0.291579061 POLA1sg2 + IKBKBsg2 + CDK4sg2 −1.696470406 1.866299793 0.272330261 EGFRsg1 + TUBA1Asg1 + HDAC1sg2 −1.690125279 1.852298952 0.277035591 MTORsg2 + PIK3C3sg2 + PIK3C3sg1 −1.687466455 1.535372763 0.078526017 MTORsg1 + TOP1sg2 + PIK3C3sg1 −1.686131993 1.391347296 0.100740203 MTORsg2 + CDK4sg3 + PIK3C3sg2 −1.683687323 1.516049873 0.045142204 TGFB1sg1 + IKBKBsg1 + TUBA1Asg2 −1.682554895 1.532602385 0.045908271 TOP1sg1 + HDAC1sg1 + TYMSsg3 −1.679150108 1.620259458 0.06372465 MTORsg1 + POLA1sg1 + IKBKBsg2 −1.678134412 1.645949082 0.027677053 TYMSsg3 + CDK4sg3 + PIK3C3sg2 −1.677611019 1.309613622 0.058702665 IKBKBsg1 + TOP1sg2 + TOP1sg2 −1.675164522 1.649411875 0.325776994 DNMT1sg2 + IKBKBsg

 + TUBA1Asg2 −1.665489364 1.736543425 0.001848481 PIK3C3sg2 + IKBKBsg2 + HDAC1sg2 −1.664281902 1.413875381 0.01631538 TOP1sg2 + dummysg1 + dummysg1 −1.659841284 1.602359306 0.052221737 IKBKBsg2 + TOP1sg2 + TYMSsg1 −1.658623009 2.107509306 0.057743531 HDAC1sg1 + IKBKBsg2 + TYMSsg3 −1.654022343 1.387716864 0.036368474 DNMT1sg1 + TUBA1Asg1 + TOP1sg2 −1.652640481 1.391855821 0.103714756 TOP1sg1 + ERBB2sg2 + TYMSsg3 −1.651915159 1.426363857 0.208862877 TOP1sg2 + POLA1sg2 + EGFRsg1 −1.64833128 1.568789899 0.061395672 TOP1sg2 + MAP2K1sg2 + dummysg2 −1.648189863 1.690274677 0.052679489 HDAC1sg

 + TYMSsg3 + ERBB2sg1 −1.647476524 1.45547239 0.091325354 POLA1sg2 + PIK3C3sg2 + MAP2K1sg2 −1.647139169 1.701316815 0.267062805 TOP1sg2 + TYMSsg1 + EGFRsg1 −1.646744424 1.82100192 0.049077865 MAP2K1sg2 + dummysg2 + PIK3C3sg2 −1.643732138 1.970725588 0.229725809 MTORsg2 + FGF2sg2 + MAP2K1sg1 −1.641297708 2.552464992 0.011724642 MTORsg1 + CDK4sg3 + MAP2K1sg2 −1.639185845 1.445401724 0.42279108 CDK4sg2 + IKBKBsg1 + PIK3C3sg2 −1.636249814 1.302253892 0.435825923 POLA1sg2 + TGFB1sg1 + IKBKBsg1 −1.635610783 1.491009974 0.085590315 DNMT1sg2 + ERBB2sg1 + EGFRsg2 −1.633220952 2.098535036 0.142769963 POLA1sg2 + TOP1sg2 + TUBA1Asg1 −1.63307072 1.442262683 0.299039452 POLA1sg2 + POLA1sg1 + FGF2sg1 −1.631821933 1.354733113 0.197871812 DNMT1sg2 + HDAC1sg2 + HDAC1sg2 −1.631724594 1.365897515 0.186479944 CDK4sg2 + CDK4sg3 + IKBKBsg1 −1.630723719 1.641643266 0.068383364 ERBB2sg1 + TUBA1Asg2 + FGF2sg1 −1.629587689 1.474675653 0.04262763 TOP1sg2 + TYMSsg1 + MAP2K1sg2 −1.62776412 1.316323822 0.256363643 TOP1sg1 + TOP1sg2 + TYMSsg1 −1.626620885 1.953066222 0.009987035 PIK3C3sg1 + PIK3C3sg1 + ERBB2sg1 −1.526590146 1.860310555 0.04737809 TUBA1Asg2 + CDK4sg3 + ERBB2sg1 −1.624671848 1.547601314 0.071441133 POLA1sg2 + FGF2sg1 + ERBB2sg2 −1.624368285 1.971484323 0.034749703 POLA1sg2 + TOP1sg2 + TYMSsg1 −1.623960314 1.308975887 0.474331002 CDK4sg3 + PIK3C3sg2 + TOP1sg2 −1.623608805 1.317903529 0.42139518 TUBA1Asg1 + TUBA1Asg2 + MTORsg1 −1.620140813 1.402365414 0.421168129 TOP1sg1 + TOP1sg2 + MAP2K1sg2 −1.619157081 1.342612232 0.4643037 TGFB1sg1 + TYMSsg1 + TYMSsg1 −1.614957919 2.590482381 0.012464342 TGFB1sg1 + TGFB1sg2 + PIK3C3sg1 −1.614802068 1.391860704 0.047099903 PIK3C3sg2 + TGFB1sg1 + IKBKBsg2 −1.614362345 1.373537621 0.169956605 IKBKBsg1 + HDAC1sg1 + IKBKBsg2 −1.61421984 1.476900256 0.085866435 MTORsg2 + POLA1sg1 + DNMT1sg2 −1.6128186 1.661041704 0.328730511 MTORsg1 + POLA1sg2 + MAP2K1sg2 −1.610897918 1.594923316 0.304366228 MTORsg1 + TOP1sg1 + EGFRsg2 −1.609025547 1.316392732 0.098652579 MAP2K1sg2 + TYMSsg3 + MTORsg2 −1.608934025 1.44352797 0.364373787 HDAC1sg2 + POLA1sg1 + HDAC1sg2 −1.604615851 1.56756982 0.019030732 POLA1sg1 + TUBA1Asg2 + MAP2K1sg1 −1.603749811 1.570377209 0.362881325 TOP1sg2 + dummysg2 + dummysg1 −1.602608416 1.724268403 0.28904057 FGF2sg1 + HDAC1sg2 + MAP2K1sg2 −1.601088009 1.645911609 0.012538686 TUBA1Asg1 + TUBA1Asg2 + TYMSsg1 −1.601033854 1.9527581 0.028671563 DNMT1sg2 + TOP1sg2 + HDAC1sg1 −1.600941062 1.426338874 0.148070775 CDK4sg2 + TOP1sg1 + EGFRsg2 −1.598154281 1.638499817 0.02188659 TGFB1sg2 + FGF2sg1 + MTORsg2 −1.597870135 1.958314433 0.00

32

148 CDK4sg2 + PIK3C3sg1 + MTORsg2 −1.596761493 1.660632513 0.251498385 TYMSsg3 + DNMT1sg1 + POLA1sg1 −1.596715385 1.305698823 0.070928906 PIK3C3sg1 + TYMSsg3 + TOP1sg2 −1.595336117 1.450560889 0.234813726 PIK3C3sg1 + EGFRsg2 + PIK3C3sg2 −1.59532899 1.531696267 0.078384502 TOP1sg1 + MTORsg1 + EGFRsg2 −1.594975223 1.459690247 0.089250811 PIK3C3sg2 + MAP2K1sg2 + HDAC1sg1 −1.592646783 1.593280479 0.0008058 dummysg2 + TUBA1Asg2 + MTORsg2 −1.592133048 1.773668138 0.011414136 TOP1sg2 + dummysg2 + HDAC1sg2 −1.590684118 1.584775981 0.293117547 ERBB2sg2 + EGFRsg1 + HDAC1sg2 −1.590128216 1.729749769 0.05350431 MTORsg2 + MAP2K1sg1 + TUBA1Asg1 −1.589379838 2.702304166 0.013562265 FGF2sg2 + EGFRsg2 + IKBKBsg2 −1.587970802 1.331711377 0.320230177 TOP1sg2 + MTORsg2 + EGFRsg2 −1.582036883 1.609073986 0.058371821 FGF2sg1 + PIK3C3sg2 + DNMT1sg2 −1.581388745 1.332054793 0.041228656 DNMT1sg1 + FGF2sg1 + TYMSsg1 −1.580583497 1.495297329 0.07818333 MTORsg1 + PIK3C2sg1 + FGF2sg2 −1.580197994 1.661886448 0.117508567 ERBB2sg1 + CDK4sg2 + TYMSsg3 −1.580170099 1.534824641 0.003543761 POLA1sg1 + DNMT1sg2 + EGFRsg1 −1.577354929 1.558280298 0.210323471 MAP2K1sg2 + HDAC1sg2 + TUBA1Asg1 −1.576617702 2.09296717 0.082457902 IKBKBsg1 + TUBA1Asg2 + HDAC1sg2 −1.572572305 1.344863438 0.221549861 dummysg1 + POLA1sg2 + TYMSsg1 −1.571598055 1.328359897 0.105950653 ERBB2sg1 + HDAC1sg1 + PIK3C3sg2 −1.570225021 1.406858491 0.089527918 MTORsg2 + PIK3C3sg1 + dummysg

−1.567665556 1.417039473 0.198545802 PIK3C3sg1 + CDK4sg3 + MAP2K1sg1 −1.566555556 1.306456876 0.113416

87 PIK3C3sg2 + TYMSsg3 + PIK3C3sg2 −1.565355811 1.435799963 0.202297882 POLA1sg1 + DNMT1sg1 + ERBB2sg1 −1.564228844 3.74229431 0.022485295 MTORsg2 + EGFRsg1 + dummysg2 −1.562673078 1.823736583 0.048241456 POLA1sg1 + DNMT1sg1 + ERBB2sg2 −1.560446602 2.004034871 0.169270894 FGF2sg1 + POLA1sg1 + ERBB2sg1 −1.55964775 1.671651203 0.004695615 FGF2sg1 + MAP2K1sg1 + TOP1sg2 −1.550656796 1.693868286 0.291652454 TYMSsg1 + DNMT1sg1 + TGFB1sg2 −1.54943741 1.627348966 0.057793234 TGFB1sg2 + EGFRsg2 + FGF2sg1 −1.549370286 1.389709517 0.083276797 TGFB1sg1 + TOP1sg2 + DNMT1sg1 −1.548423999 1.487833829 0.26747628 PIK3C3sg1 + ERBB2sg2 + TYMSsg1 −1.547599357 1.372969309 0.02417538 HDAC1sg2 + TOP1sg2 + EGFRsg1 −1.547020551 1.538200993 0.075571384 MTORsg1 + TOP1sg1 + TYMSsg3 −1.541645305 1.526548277 0.022044896 MTORsg2 + POLA1sg1 + ERBB2sg2 −1.540871299 2.466751441 0.009646202 EGFRsg2 + POLA1sg2 + FGF2sg2 −1.539877498 1.76598257 0.017190333 ERBB2sg1 + TUBA1Asg2 + MAP2K1sg1 −1.537149386 1.355762594 0.216997889 TYMSsg3 + MAP2K1sg1 + EGFRsg2 −1.536201879 1.605144785 0.335270544 FGF2sg1 + EGFRsg2 + TUBA1Asg1 −1.535904088 1.388183429 0.04449609 FGF2sg2 + TYMSsg3 + EGFRsg1 −1.533403223 1.628088812 0.024474729 POLA1sg2 + HDAC1sg2 + DNMT1sg2 −1.533045741 1.597839629 0.250479593 MTORsg2 + TUBA1Asg1 + CDK4sg2 −1.532058917 1.384955805 0.162734407 DNMT1sg1 + ERBB2sg1 + HDAC1sg

−1.530734859 1.412361024 0.323047044 EGFRsg2 + POLA1sg2 + TYMSsg3 −1.529687156 1.402844708 0.089283636 MAP2K1sg1 + ERBB2sg1 + HDAC1sg2 −1.527557082 1.645220091 0.31642287 MAP2K1sg2 + TUBA

Asg1 + TYMSsg3 −1.525567613 1.436821229 0.096068303 DNMT1sg2 + MTORsg2 + PIK3C3sg2 −1.523222057 2.531418201 0.00929079 ERBB2sg1 + TOP1sg2 + ERBB2sg2 −1.52308012 2.042124444 0.199706618 TYMSsg3 + dummysg2 + TOP1sg2 −1.522966972 2.019637833 0.074904966 TGFB1sg2 + TGFB1sg1 + TYMSsg3 −1.518155487 1.9701

5255 0.067866886 dummysg2 + MAP2K1sg1 + DNMT

sg2 −1.517628561 1.425656021 0.034822421 MAP2K1sg2 + IKBKBsg2 + TOP1sg2 −1.51573696 1.323577069 0.07349397 PIK3C3sg2 + FGF2sg1 + POLA1sg1 −1.511782124 2.531299074 0.012411058 DNMT1sg2 + ERBB2sg2 + TUBA1Asg1 −1.511732742 1.830685607 0.181579204 MAP2K1sg2 + TGFB1sg1 + TOP1sg2 −1.509556332 1.75823374 0.033977528 MAP2K1sg1 + MTORsg1 + CDK4sg3 −1.509379602 1.465437249 0.068086672 EGFRsg1 + TYMSsg3 + MTORsg1 −1.505814152 1.399784155 0.091247402 dummysg1 + TUBA1Asg2 + EGFRsg2 −1.505781069 1.332573405 0.322591239 PIK3C3sg2 + POLA1sg2 + FGF2sg1 −1.502997493 1.727046904 0.045534473 PIK3C3sg1 + MTORsg1 + DNMT1sg2 −1.50275768 2.093830085 0.029495577 MTORsg2 + MTORsg2 + DNMT1sg2 −1.501972528 1.422359397 0.387319237 MTORsg2 + IKBKBsg1 + TYMSsg1 −1.501912524 1.365293732 0.376649027 PIK3C3sg2 + PIK3C3sg2 + TYMSsg1 −1.499631682 1.448691353 0.263783234 dummysg1 + POLA1sg2 + TYMSsg3 −1.4981151 1.309754391 0.460094538 MAP2K1sg2 + HDAC1sg2 + DNMT1sg2 −1.496780144 1.896700017 0.229692681 MAP2K1sg2 + TYMSsg1 + PIK3C3sg1 −1.495986207 1.477757285 0.072448091 HDAC1sg1 + MTORsg1 + TYMSsg3 −1.495827678 1.490781875 0.078750162 TYMSsg3 + EGFRsg2 + TOP1sg2 −1.49561846 2.43042514 0.006425892 TOP1sg2 + FGF2sg1 + TGFB1sg1 −1.495322213 1.580102068 0.063389085 PIK3C3sg2 + TOP1sg2 + IKBKBsg1 −1.495146589 1.982339277 0.034375456 TUBA1Asg1 + TYMSsg1 + TYMSsg3 −1.495105405 1.557373315 0.324055235 TYMSsg3 + TUBA1Asg2 + PIK3C3sg2 −1.494985267 1.609816245 0.27366 PIK3C3sg2 + FGF2sg2 + TUBA1Asg2 −1.492413348 1.308846511 0.07465639 TOP1sg2 + DNMT1sg1 + DNMT1sg1 −1.491316488 1.315399728 0.202321382 TUBA1Asg1 + MTORsg1 + PIK3C3sg2 −1.490409009 2.447377188 0.100655238 HDAC1sg2 + MAP2K1sg1 + FGF2sg2 −1.485790765 1.432470195 0.06399842 IKBKBsg

 + POLA1sg1 + TYMSsg1 −1.482797631 1.498148348 0.22973

062 TOP1sg1 + PIK3C3sg2 + MAP2K1sg2 −1.482167694 1.401435053 0.324497592 POLA1sg2 + EGFRsg1 + dummysg1 −1.479874715 1.357191632 0.068490903 TYMSsg3 + PIK3C3sg1 + POLA1sg1 −1.479864639 2.157062206 0.134413435 IKBKBsg1 + POLA1sg1 + dummysg2 −1.479703819 2.15570599 0.024766198 TUBA1Asg1 + TYMSsg3 + DNMT1sg2 −1.477410505 1.693643881 0.045139189 POLA1sg2 + DNMT1sg1 + FGF2sg2 −1.477222477 2.150744231 0.092750843 PIK3C3sg1 + HDAC1sg2 + TYMSsg3 −1.477182488 1.706892107 0.058895791 DNMT1sg2 + TYMSsg3 + TYMSsg3 −1.476595475 1.431787373 0.086328481 dummysg2 + PIK3C3sg2 + POLA1sg1 −1.474370596 2.60232275 0.102048575 TUBA1Asg2 + ERBB2sg2 + ERBB2sg2 −1.474290532 1.47081

12 0.275490842 TOP1sg1 + dummysg1 + TGFB1sg1 −1.473301784 1.663093137 0.042345865 TOP1sg1 + TOP1sg2 + TUBA1Asg1 −1.473281557 1.679342532 0.294246485 TYMSsg3 + ERBB2sg1 + HDAC1sg1 −1.470883315 2.004846202 0.065165246 TUBA1Asg1 + MAP2K1sg1 + MAP2K1sg1 −1.469789014 2.580748659 0.014684728 dummysg1 + POLA1sg2 + dummysg2 −1.468989782 1.307127408 0.103621048 DNMT1sg2 + HDAC1sg2 + MAP2K1sg2 −1.466310813 1.334190282 0.100585418 TOP1sg1 + ERBB2sg1 + IKBKBsg2 −1.464978257 1.765930022 0.256413313 IKBKBsg2 + FGF2sg1 + TOP1sg2 −1.461044698 1.36689808 0.001663924 EGFRsg1 + TUBA1Asg2 + TOP1sg2 −1.460505781 1.349122827 0.121796173 MTORsg2 + TYMSsg3 + IKBKBsg2 −1.46029389 1.56511863 0.066455704 ERBB2sg2 + ERBB2sg2 + MTORsg2 −1.45946274 1.578728

0.315409893 HDAC1sg1 + ERBB2sg2 + HDAC1sg2 −1.45891216 3.794962068 0.002795435 ERBB2sg1 + EGFRsg2 + DNMT1sg2 −1.458296767 1.314455125 0.034672861 FGF2sg1 + CDK4sg2 + TOP1sg2 −1.457096934 2.145998683 0.093734226 POLA1sg1 + ERBB2sg1 + CDK4sg2 −1.452286035 3.102895819 0.054615659 TYMSsg1 + MTORsg1 + EGFRsg1 −1.451874923 1.438738465 0.013805962 MAP2K1sg1 + PIK3C3sg1 + POLA1sg1 −1.451797293 1.503162372 0.023301537 POLA1sg2 + EGFRsg1 + PIK3C3sg1 −1.45179701 2.730144583 0.008231665 POLA1sg1 + CDK4sg3 + dummysg2 −1.446932566 1.62969787 0.171868324 MTORsg1 + DNMT1sg1 + DNMT1sg2 −1.446574928 2.397787511 0.097031509 TUBA1Asg1 + TYMSsg3 + TYMSsg

−1.445338938 2.458077932 0.007001913 ERBB2sg1 + TGFB1sg1 + MAP2K1sg1 −1.444654448 1.827144257 0.01215679 TUBA1Asg2 + FGF2sg2 + PIK3C3sg2 −1.437793063 1.496974422 0.000818024 MTORsg1 + MAP2K1sg1 + HDAC1sg1 −1.435623217 1.933152413 0.200263554 TYMSsg3 + TYMSsg1 + ERBB2sg2 −1.43269356 1.490092485 0.06548439 TOP1sg2 + FGF2sg2 + HDAC1sg2 −1.430017235 2.945707693 0.06587704 POLA1sg2 + PIK3C3sg1 + TYMSsg1 −1.429

45368 1.311709006 0.051252767 TGFB1sg1 + TUBA1Asg1 + FGF2sg1 −1.429572703 2.141902997 0.001541075 CDK4sg3 + IKBKBsg2 + ERBB2sg1 −1.427986397 1.694791766 0.050344835 FGF2sg1 + FGF2sg2 + TOP1sg2 −1.4279651 1.829982829 0.233988873 EGFRsg1 + HDAC1sg1 + CDK4sg2 −1.427818139 1.481983047 0.076503749 MTORsg2 + DNMT1sg2 + MAP2K1sg1 −1.427413579 2.494875891 0.048600762 TOP1sg2 + PIK3C3sg1 + TYMSsg3 −1.426554117 1.537830054 0.068827798 TOP1sg1 + TUBA1Asg2 + PIK3C3sg2 −1.425911098 1.688269649 0.266628514 EGFRsg1 + TYMSsg3 + TYMSsg3 −1.424477158 1.998262928 0.026147664 MTORsg2 + ERBB2sg1 + PIK3C3sg2 −1.422173273 1.330125852 0.135032832 IKBKBsg2 + POLA1sg2 + MAP2K1sg2 −1.421854053 1.387658346 0.323258114 TOP1sg2 + PIK3C3sg2 + ERBB2sg1 −1.421033006 1.319052145 0.060090301 DNMT1sg1 + TYMSsg1 + PIK3C3sg1 −1.420787597 1.624344459 0.178367455 ERBB2sg1 + TUBA1Asg2 + IKBKBsg2 −1.420224028 1.648232567 0.042041485 EGFRsg1 + HDAC1sg2 + TOP1sg2 −1.420004206 1.501342512 0.064387826 MTORsg1 + TOP1sg2 + HDAC1sg1 −1.4176314 1.474088236 0.018029297 EGFRsg1 + DNMT1sg1 + MTORsg2 −1.41354047 1.615008501 0.262789329 DNMT1sg2 + POLA1sg1 + EGFRsg1 −1.412166526 1.377401536 0.24693009 IKBKBsg1 + HDAC1sg1 + ERBB2sg2 −1.409196173 1.393629919 0.012128297 PIK3C3sg1 + PIK3C3sg2 + CDK4sg3 −1.406535054 1.647291564 0.04

823198 POLA1sg1 + FGF2sg1 + dummysg2 −1.405411163 2.228989644 0.022617066 EGFRsg1 + DNMT1sg2 + PIK3C3sg2 −1.403101248 1.

36948008 0.039504281 TOP1sg1 + TYMSsg3 + FGF2sg1 −1.401673011 1.859107157 0.18473325 PIK3C3sg1 + ERBB2sg2 + ERBB2sg1 −1.400938826 1.555893934 0.274968569 MTORsg1 + PIK3C3sg2 + EGFRsg1 −1.399330923 1.607792213 0.148472893 TOP1sg2 + IKBKBsg1 + dummysg1 −1.399132481 1.52872237 0.069539706 TOP1sg2 + TOP1sg1 + HDAC1sg1 −1.396510294 1.794178752 0.245400821 CDK4sg2 + TYMSsg3 + POLA1sg1 −1.396234434 1.42651631 0.376100013 POLA1sg1 + TUBA1Asg2 + dummysg2 −1.394381808 1.543453406 0.078474735 IKBKBsg1 + MTORsg2 + FGF2sg2 −1.391641648 1.

24285225 0.126398472 TYMSsg3 + HDAC1sg1 + TUBA1Asg2 −1.387362148 1.581346164 0.293826192 TOP1sg1 + POLA1sg1 + TGFB1sg1 −1.387291361 2.184351279 0.142091894 POLA1sg1 + FGF2sg2 + EGFRsg1 −1.386864657 1.352853646 0.069428613 MTORsg1 + MAP2K1sg2 + EGFRsg2 −1.386280066 1.319643975 0.181544092 MTORsg1 + DNMT1sg1 + HDAC1sg1 −1.385920316 1.443864068 0.348140672 TGFB1sg1 + TUBA1Asg1 + PIK3C3sg2 −1.384318373 1.743602195 0.020213909 MAP2K1sg1 + TGFB1sg1 + PIK3C3sg2 −1.382758662 3.280835056 0.040141456 FGF2sg1 + POLA1sg2 + MAP2K1sg2 −1.381789027 1.679799264 0.269846231 PIK3C3sg2 + dummysg2 + POLA1sg1 −1.380937544 1.382034514 0.087504744 MAP2K1sg1 + IKBKBsg1 + MTORsg2 −1.378664386 1.33181113 0.156909826 TYMSsg1 + FGF2sg1 + IKBKBsg1 −1.377886415 1.495628444 0.038381775 MTORsg1 + ERBB2sg2 + HDAC1sg1 −1.375376009 1.91521752 0.008451516 POLA1sg1 + EGFRsg1 + TYMSsg3 −1.375354315 1.572618258 0.304817076 CDK4sg3 + TOP1sg2 + CDK4sg2 −1.375148814 1.304558091 0.167931826 HDAC1sg1 + TUBA1Asg2 + PIK3C3sg2 −1.374968473 1.69337672 0.161300844 TGFB1sg1 + PIK3C3sg1 + TYMSsg1 −1.370759508 1.334507067 0.091460897 MAP2K1sg1 + PIK3C3sg1 + TOP1sg2 −1.36742420

1.524853738 0.163295413 FGF2sg2 + FGF2sg2 + TOP1sg2 −1.366466681 1.331441838 0.373247474 CDK4sg2 + POLA1sg1 + TYMSsg3 −1.365408749 3.938637927 0.01904496 MAP2K1sg2 + TUBA1Asg2 + PIK3C3sg2 −1.365225643 1.320398057 0.097427051 POLA1sg2 + DNMT1sg2 + TGFB1sg1 −1.363995609 1.506269441 0.33481059 ERBB2sg2 + MTORsg2 + TYMSsg3 −1.363951639 1.508327536 0.265903089 MAP2K1sg2 + IKBKBsg1 + TGFB1sg2 −1.361795165 1.432528236 0.136574254 POLA1sg2 + EGFRsg2 + DNMT1sg2 −1.360065102 1.841327836 0.018481742 EGFRsg2 + TGFB1sg2 + EGFRsg1 −1.358882953 1.303770539 0.098605783 FGF2sg1 + ERBB2sg2 + MTORsg2 −1.355415734 1.31681812 0.339528502 POLA1sg1 + CDK4sg3 + DNMT1sg2 −1.354631037 3.731876145 0.008843321 dummysg2 + FGF2sg2 + TUBA1Asg2 −1.352460688 1.448489694 0.003319819 TOP1sg2 + TOP1sg2 + HDAC1sg2 −1.352359969 1.374259224 0.000493967 FGF2sg2 + DNMT1sg1 + TOP1sg2 −1.352163936 1.469395655 0.168557552 HDAC1sg2 + PIK3C3sg2 + TGFB1sg1 −1.351375897 1.639462552 0.254266218 MAP2K1sg1 + TGFB1sg1 + TYMSsg1 −1.351337642 2.130534843 0.160411893 MTORsg1 + CDK4sg2 + PIK3C3sg2 −1.349747186 1.805085512 0.016730567 FGF2sg2 + TGFB1sg1 + TOP1sg2 −1.347559924 1.714175087 0.035284923 DNMT1sg2 + HDAC1sg2 + TGFB1sg1 −1.347359609 1.659849875 0.255133525 TUBA1Asg1 + HDAC1sg2 + PIK3C3sg2 −1.345794422 2.203105276 0.117108263 TGFB1sg2 + EGFRsg1 + IKBKBsg2 −1.345774957 2.116664335 0.108526837 TYMSsg3 + HDAC1sg2 + PIK3C3sg1 −1.345424347 1.846906883 0.220628478 MAP2K1sg1 + TOP1sg2 + TYMSsg1 −1.344948696 1.398764639 0.112491542 HDAC1sg2 + DNMT1sg1 + PIK3C3sg2 −1.344921487 1.411763679 0.008329094 EGFRsg2 + dummysg1 + TGFB1sg1 −1.344695737 1.583663094 0.054144193 TUBA1Asg1 + CDK4sg3 + FGF2sg2 −1.343957794 1.74093954 0.038110015 TYMSsg3 + MTORsg1 + MAP2K1sg1 −1.343780707 1.650692627 0.052441531 TGFB1sg2 + FGF2sg2 + PIK3C3sg1 −1.343362119 1.369735894 0.083950087 dummysg1 + TOP1sg2 + HDAC1sg1 −1.341599556 1.473934692 0.219243248 MAP2K1sg2 + PIK3C3sg1 + IKBKBsg1 −1.341089876 1.345468648 0.314004914 TYMSsg3 + TYMSsg3 + POLA1sg2 −1.340443392 1.42296827 0.079082304 FGF2sg2 + FGF2sg1 + EGFRsg1 −1.338695369 1.343573603 0.075181345 POLA1sg2 + TYMSsg3 + TGFB1sg2 −1.338345124 1.706678146 0.031668144 MAP2K1sg1 + ERBB2sg2 + HDAC1sg2 −1.33830546 1.427153303 0.350982135 PIK3C3sg2 + TUBA1Asg2 + TYMSsg3 −1.3380872 1.405584092 0.092751704 TGFB1sg2 + EGFRsg2 + TUBA1Asg1 −1.336183129 1.4927078 0.289662201 ERBB2sg2 + PIK3C3sg2 + ERBB2sg1 −1.335502314 1.799816889 0.227223021 ERBB2sg1 + TOP1sg2 + TYMSsg1 −1.334795009 2.996639786 0.007346517 PIK3C3sg2 + CDK4sg2 + EGFRsg2 −1.33455415 1.8324318

3 0.033270989 DNMT1sg2 + TOP1sg2 + PIK3C3sg2 −1.333627929 2.625642273 0.007336883 PIK3C3sg2 + ERBB2sg1 + EGFRsg2 −1.332456352 1.602058249 0.014183678 TGFB1sg1 + TOP1sg1 + MAP2K1sg2 −1.331862236 1.691298099 0.04446819 POLA1sg2 + PIK3C3sg2 + MAP2K1sg1 −1.329515049 1.493657076 0.171297304 TGFB1sg1 + FGF2sg1 + dummysg2 −1.328457981 1.45543412 0.068463828 TYMSsg3 + MTORsg2 + IKBKBsg1 −1.32738737 1.357736781 0.184653564 EGFRsg1 + POLA1sg2 + EGFRsg2 −1.325995333 2.043080659 0.047338945 ERBB2sg2 + TOP1sg2 + FGF2sg2 −1.320749668 1.340407455 0.362104926 EGFRsg1 + dummysg2 + TYMSsg3 −1.320454859 1.622788812 0.040549009 TYMSsg3 + CDK4sg3 + HDAC1sg2 −1.319316043 1.749235363 0.221321275 dummysg2 + IKBKBsg1 + TYMSsg1 −1.318986557 1.307079246 0.256592669 ERBB2sg2 + TOP1sg1 + PIK3C3sg2 −1.318545944 1.820102018 0.026869423 TOP1sg1 + PIK3C3sg1 + IKBKBsg2 −1.318324076 1.951974738 0.016474409 MTORsg1 + dummysg2 + TYMSsg3 −1.316482389 2.27979998 0.00

311752 PIK3C3sg2 + DNMT1sg1 + EGFRsg1 −1.315642765 1.30522282 0.151339996 TOP1sg2 + ERBB2sg2 + ERBB2sg1 −1.314443136 1.953902293 0.191045189 MTORsg1 + EGFRsg2 + DNMT1sg1 −1.311885214 1.397997646 0.26894441 POLA1sg1 + DNMT1sg1 + EGFRsg2 −1.311800013 1.709342073 0.037993177 IKBKBsg2 + TOP1sg1 + DNMT1sg1 −1.311098942 1.705120455 0.038280572 EGFRsg1 + POLA1sg2 + ERBB2sg2 −1.310938738 2.340316485 0.072870879 ERBB2sg1 + TGFB1sg1 + DNMT1sg1 −1.31085141 1.421636095 0.074799255 MAP2K1sg2 + TOP1sg2 + PIK3C3sg2 −1.309848718 1.367651652 0.048791892 DNMT1sg2 + MAP2K1sg1 + HDAC1sg1 −1.30899509 2.786779563 0.055409746 TYMSsg3 + MTORsg2 + dummysg1 −1.308604645 2.80433135 0.0718836 EGFRsg2 + MTORsg2 + DNMT1sg1 −1.3062803 1.326459684 0.396036204 TOP1sg2 + DNMT1sg1 + dummysg1 −1.300960967 1.528702335 0.271133817 IKBKBsg2 + ERBB2sg2 + CDK4sg2 −1.300876711 1.501235853 0.066000681 MTORsg2 + TYMSsg3 + ERBB2sg2 −1.298955214 1.676022472 0.054357807 PIK3C3sg1 + dummysg2 + PIK3C3sg1 −1.297665157 1.41639969 0.323904599 EGFRsg1 + ERBB2sg1 + FGF2sg2 −1.296278927 1.589277845 0.073560052 ERBB2sg1 + PIK3C3sg2 + ERBB2sg2 −1.294858405 1.389771833 0.079932689 dummysg1 + dummysg2 + PIK3C3sg2 −1.294261192 1.754960093 0.01438107 HDAC1sg1 + TUBA1Asg1 + PIK3C3sg2 −1.293970402 2.070482285 0.117130807 MTORsg2 + ERBB2sg1 + dummysg2 −1.293731407 1.865866071 0.02101871 ERBB2sg1 + HDAC1sg2 + EGFRsg1 −1.292890584 1.540049449 0.022273947 IKBKBsg1 + TUBA1Asg2 + ERBB2sg2 −1.290940246 1.51539624 0.314060367 EGFRsg2 + DNMT1sg1 + ERBB2sg1 −1.280957513 2.450254951 0.002138527 PIK3C3sg1 + POLA1sg2 + PIK3C3sg2 −1.280863277 1.899762551 0.031169898 POLA1sg2 + TOP1sg2 + PIK3C3sg2 −1.27929807 1.37041105 0.356425212 TOP1sg2 + TOP1sg2 + HDAC1sg1 −1.279245755 1.588179279 0.053735323 dummysg1 + CDK4sg2 + HDAC1sg1 −1.277378063 1.419467858 0.123871497 FGF2sg1 + TYMSsg1 + DNMT1sg2 −1.275469819 1.393836109 0.079832849 TGFB1sg1 + POLA1sg1 + TGFB1sg1 −1.274978295 1.481745644 0.00844416 MTORsg1 + FGF2sg1 + FGF2sg2 −1.272114528 1.449836483 0.069588295 CDK4sg3 + MTORsg1 + MAP2K1sg2 −1.271655871 1.760270924 0.074808917 IKBKBsg2 + dummysg1 + FGF2sg1 −1.271222092 1.382706598 0.181996815 dummysg1 + TOP1sg1 + MAP2K1sg2 −1.269439426 2.076563485 0.113323724 CDK4sg3 + MTORsg2 + TUBA1Asg1 −1.268239319 1.664273687 0.259108117 TOP1sg1 + EGFRsg1 + IKBKBsg1 −1.265879358 1.81491055 0.003175503 IKBKBsg1 + POLA1sg2 + TYMSsg3 −1.265685068 1.318126386 0.028571307 dummysg2 + EGFRsg1 + TYMSsg3 −1.265538935 1.815661773 0.031726364 POLA1sg2 + CDK4sg3 + ERBB2sg2 −1.265086633 2.128642052 0.01945501 POLA1sg2 + TOP1sg2 + ERBB2sg2 −1.264814004 1.433457463 0.235822813 EGFRsg1 + POLA1sg1 + POLA1sg1 −1.264585326 1.820209337 0.037915014 IKBKBsg1 + MTORsg1 + ERBB2sg1 −1.264142405 1.44141307 0.274612754 DNMT1sg1 + TOP1sg2 + CDK4sg2 −1.262532147 1.376521193 0.360058703 TYMSsg1 + TUBA1Asg2 + ERBB2sg1 −1.260374249 1.582637795 0.25535132 POLA1sg1 + TOP1sg2 + ERBB2sg2 −1.259615106 1.499919489 0.05181229 TYMSsg3 + FGF2sg1 + DNMT1sg1 −1.258792121 2.32139693 0.018452661 PIK3C3sg1 + dummysg2 + FGF2sg1 −1.257162892 1.541741855 0.056108994 CDK4sg3 + CDK4sg3 + ERBB2sg1 −1.255640017 1.47455108 0.067532974 TGFB1sg2 + IKBKBsg1 + TYMSsg1 −1.254024141 1.372755332 0.353746448 dummysg2 + TOP1sg2 + CDK4sg2 −1.249716897 1.323644563 0.07620

64

POLA1sg1 + FGF2sg1 + CDK4sg2 −1.248097293 1.59799095 0.052142212 PIK3C3sg2 + dummysg2 + TYMSsg1 −1.247310482 1.479737336 0.23384087 TOP1sg2 + dummysg2 + HDAC1sg1 −1.246790234 1.418504573 0.137226342 PIK3C3sg2 + TOP1sg2 + PIK3C3sg1 −1.245453399 1.472001335 0.105354175 IKBKBsg1 + ERBB2sg1 + PIK3C3sg1 −1.243125192 1.41359982 0.167143163 EGFRsg1 + CDK4sg2 + TOP1sg2 −1.241792396 1.409884815 0.262811019 TUBA1Asg2 + POLA1sg1 + PIK3C3sg2 −1.240477141 1.842080795 0.197905958 MTORsg2 + ERBB2sg2 + EFGRsg2 −1.239790736 1.70860978 0.021340993 PIK3C3sg1 + ERBB2sg2 + HDAC1sg2 −1.239155414 1.671081784 0.031982756 TYMSsg3 + EGFRsg2 + ERBB2sg1 −1.239124149 1.504027279 0.26069021 TYMSsg3 + dummysg1 + ERBB2sg1 −1.239089747 1.42588972 0.303138673 IKBKBsg1 + dummysg2 + POLA1sg2 −1.238117943 1.320435936 0.085189353 POLA1sg2 + FGF2sg2 + PIK3C3sg1 −1.237820837 1.435889323 0.071

7167

MAP2K1sg2 + TOP1sg2 + dummysg2 −1.235456171 1.64927995 0.049985801 TYMSsg3 + TOP1sg2 + TYMSsg3 −1.233746277 2.2

7716349 0.019008981 TOP1sg1 + MTORsg2 + TGFB1sg1 −1.233202088 1.524108864 0.0536816 HDAC1sg1 + TOP1sg1 + EGFRsg1 −1.232283395 1.93702361 0.023159087 TOP1sg1 + TGFB1sg2 + dummysg2 −1.230841396 1.814725563 0.182197459 HDAC1sg2 + PIK3C3sg2 + TYMSsg3 −1.229407576 1.490204986 0.3090415 PIK3C3sg2 + FGF2sg2 + PIK3C3sg2 −1.228057218 1.765550422 0.041858683 HDAC1sg1 + CDK4sg3 + IKBKBsg1 −1.227824044 1.471131502 0.046345733 TOP1sg1 + dummysg2 + POLA1sg1 −1.227455645 1.787449747 0.217504593 PIK3C3sg2 + TOP1sg2 + FGF2sg2 −1.226395789 1.404893669 0.308538318 TGFB1sg1 + POLA1sg

 + TYMSsg1 −1.225148726 1.45360168 0.024121865 PIK3C3sg2 + EGFRsg1 + TGFB1sg1 −1.224620861 1.479560518 0.28752632 POLA1sg2 + TYMSsg3 + IKBKBsg1 −1.223030103 1.571442764 0.050949206 TGFB1sg1 + TGFB1sg2 + TYMSsg3 −1.220555595 2.283123647 0.095619751 IKBKBsg2 + PIK3C3sg1 + TYMSsg3 −1.220158724 1.302842793 0.115673346 MAP2K1sg1 + POLA1sg2 + POLA1sg1 −1.219932651 1.378740376 0.074629057 MAP2K1sg1 + dummysg2 + TUBA1Asg2 −1.219137021 2.572884493 0.011934954 TGFB1sg1 + IKBKBsg1 + EGFRsg1 −1.219127234 1.630691855 0.17368992 ERBB2sg1 + TUBA1Asg1 + FGF2sg2 −1.218956334 1.377996522 0.255670723 ERBB2sg2 + dummysg2 + ERBB2sg1 −1.218638323 1.382031658 0.342549739 MTORsg1 + DNMT1sg2 + dummysg1 −1.217225073 1.486148813 0.270153319 DNMT1sg2 + MTORsg2 + IKBKBsg1 −1.214747774 1.709051852 0.236670401 ERBB2sg1 + TOP1sg2 + PIK3C3sg2 −1.213065536 2.011280735 0.026018056 TYMSsg3 + POLA1sg1 + dummysg1 −1.212915658 1.356924534 0.076848262 FGF2sg2 + FGF2sg1 + EGFRsg2 −1.21002715 1.353365865 0.08056483 TOP1sg1 + TYMSsg3 + CDK4sg3 −1.206991596 1.411222117 0.326214068 MTORsg2 + HDAC1sg2 + ERBB2sg2 −1.205650813 1.324777463 0.081229653 TUBA1Asg1 + POLA1sg1 + dummysg2 −1.205531407 1.759552155 0.041219075 IKBKBsg1 + FGF2sg1 + EGFRsg2 −1.204684543 1.305017526 0.228302359 TYMSsg3 + MAP2K1sg2 + DNMT1sg2 −1.204532453 1.921598228 0.017361785 IKBKBsg2 + HDAC1sg1 + PIK3C3sg2 −1.204373015 1.392220102 0.233735487 PIK3C3sg2 + TUBA1Asg2 + TOP1sg2 −1.202930221 1.356980498 0.068603519 MAP2K1sg2 + TUBA1Asg2 + TUBA1Asg1 −1.199685367 1.328622127 0.092828228 DNMT1sg2 + POLA1sg1 + HDAC1sg2 −1.197895553 1.32751666 0.234588416 EGFRsg2 + FGF2sg2 + POLA1sg2 −1.19739853 1.577230721 0.008430165 EGFRsg1 + TYMSsg3 + DNMT1sg2 −1.195960218 2.20782217 0.020304266 IKBKBsg1 + POLA1sg2 + FGF2sg2 −1.195700675 1.463525122 0.047214298 dummysg3 + IKBKBsg1 + MTORsg1 −1.194389646 2.328415056 0.016898954 IKBKBsg1 + dummysg2 + TYMSsg3 −1.193288111 1.441210318 0.139659167 TYMSsg3 + HDAC1sg1 + ERBB2sg1 −1.192880943 2.278962566 0.012585095 POLA1sg2 + EGFRsg1 + FGF2sg1 −1.192673959 1.707812003 0.027120506 TGFB1sg1 + IKBKBsg1 + TYMSsg3 −1.192237955 1.435511546 0.091554439 DNMT1sg1 + TOP1sg2 + TYMSsg3 −1.19054239 1.524187489 0.059634492 CDK4sg3 + TYMSsg3 + TYMSsg3 −1.189307836 1.772768737 0.213

5807 ERBB2sg1 + TOP1sg2 + MAP2K1sg2 −1.188900726 1.421898036 0.271612

5

IKBKBsg2 + FGF2sg1 + TYMSsg1 −1.188517618 1.368270351 0.03442971 IKBKBsg2 + TGFB1sg1 + EGFRsg1 −1.186509796 1.413341324 0.041476937 IKBKBsg2 + TYMSsg3 + TUBA1Asg1 −1.185706347 1.522532157 0.277831557 DNMT1sg2 + MAP2K1sg1 + DNMT1sg1 −1.182824215 2.631235987 0.072935446 HDAC1sg1 + TUBA1Asg2 + POLA1sg2 −1.181015558 1.340061865 0.077963637 TYMSsg3 + TUBA1Asg2 + EGFRsg1 −1.180098177 1.858564323 0.051987208 PIK3C3sg2 + PIK3C3sg2 + PIK3C3sg1 −1.180045809 1.430729026 0.111264144 HDAC1sg1 + dummysg2 + TYMSsg1 −1.178675401 1.646706405 0.203366324 TYMSsg3 + DNMT1sg2 + HDAC1sg2 −1.178611555 2.420102783 0.008444286 HDAC1sg2 + TOP1sg2 + TYMSsg1 −1.178607323 1.672195465 0.046222202 PIK3C3sg2 + TGFB1sg1 + HDAC1sg2 −1.178435553 2.030439308 0.003561127 dummysg2 + POLA1sg2 + CDK4sg2 −1.177540653 2.100213537 0.015361341 ERBB2sg2 + TOP1sg1 + POLA1sg1 −1.177420689 1.327039273 0.082902213 CDK4sg2 + EGFRsg1 + FGF2sg1 −1.176861069 1.790915241 0.025866391 PIK3C3sg2 + IKBKBsg2 + EGFRsg2 −1.176558624 2.130744362 0.122029064 MTORsg1 + dummysg2 + EGFRsg1 −1.176235111 2.110203063 0.013354705 MTORsg1 + FGF2sg1 + TYMSsg3 −1.173971623 1.440849509 0.174920347 HDAC1sg1 + TUBA1Asg2 + TYMSsg1 −1.173202075 2.400431617 0.005874075 MTORsg2 + dummysg2 + MAP2K1sg2 −1.171601676 1.311471947 0.34675857 HDAC1sg2 + PIK3C3sg2 + DNMT1sg1 −1.17093857 1.365987965 0.076229676 TYMSsg1 + TUBA1Asg2 + MAP2K1sg1 −1.169999477 2.744294603 0.002745238 POLA1sg2 + FGF2sg1 + HDAC1sg1 −1.169377038 2.747871382 0.00

377961 dummysg2 + TUBA1Asg2 + ERBB2sg1 −1.169242129 1.309999186 0.251486673 EGFRsg1 + TOP1sg2 + TUBA1Asg1 −1.169043477 1.39323852 0.065944266 dummysg2 + POLA1sg2 + HDAC1sg1 −1.168765223 1.620074804 0.184724275 MAP2K1sg1 + MAP2K1sg1 + TGFB1sg2 −1.168138803 1.444668026 0.010394806 HDAC1sg1 + DNMT1sg1 + POLA1sg1 −1.164911043 2.410573528 0.025309821 CDK4sg3 + TOP1sg

 + TOP1sg1 −1.164788152 1.464877393 0.152143438 CDK4sg3 + IKBKBsg1 + PIK3C3sg2 −1.163469132 2.403148093 0.06819063 EGFRsg2 + PIK3C3sg1 + HDAC1sg2 −1.163353808 1.421757488 0.145341713 DNMT1sg2 + DNMT1sg1 + CDK4sg2 −1.163237176 1.31103415 0.073585849 POLA1sg1 + PIK3C3sg2 + dummysg2 −1.163220009 2.527702891 0.022767753 MAP2K1sg1 + ERBB2sg2 + CDK4sg2 −1.162854275 1.394671411 0.06787384 dummysg1 + TYMSsg1 + CDK4sg3 −1.162709705 2.107084729 0.142580135 TGFB1sg1 + TYMSsg1 + HDAC1sg1 −1.162413115 1.958211422 0.025929662 dummysg1 + PIK3C3sg1 + DNMT1sg2 −1.16213838 2.729026552 0.009588739 MTORsg2 + CDK4sg3 + dummysg1 −1.161232245 1.58980798 0.019203264 TUBA1Asg1 + FGF2sg1 + FGF2sg1 −1.160041526 2.608901154 0.011142575 ERBB2sg1 + DNMT1sg1 + HDAC1sg2 −1.15925313 1.519956462 0.264694678 TYMSsg3 + TOP1sg2 + TGFB1sg

−1.15780408 1.309744865 0.291740995 PIK3C3sg2 + dummysg2 + EGFRsg

−1.156621586 1.424093355 0.055544166 TYMSsg3 + POLA1sg2 + DNMT1sg1 −1.15642376 3.04933 0.039109322 DNMT1sg1 + TUBA1Asg1 + TYMSsg3 −1.155920071 1.435181357 0.300986546 PIK3C3sg2 + IKBKBsg2 + EGFRsg1 −1.153933918 1.555304295 0.019061329 CDK4sg3 + PIK3C3sg2 + EGFRsg1 −1.151981286 1.75575908 0.030279932 POLA1sg1 + IKBKBsg2 + CDK4sg3 −1.15045991 1.935660928 0.061112748 CDK4sg3 + HDAC1sg2 + TYMSsg1 −1.149759849 2.0552381 0.033733694 IKBKBsg1 + EGFRsg2 + EGFRsg1 −1.149566926 1.3691793 0.075927108 MAP2K1sg1 + HDAC1sg1 + DNMT1sg1 −1.146426378 1.865859731 0.032574646 POLA1sg2 + FGF2sg2 + TOP1sg2 −1.146293299 1.529822919 0.22141236 ERBB2sg1 + EGFRsg1 + ERBB2sg2 −1.145412116 1.355569791 0.335781588 POLA1sg2 + DNMT1sg1 + ERBB2sg1 −1.144655413 1.537209789 0.018875104 MTORsg1 + POLA1sg2 + TGFB1sg2 −1.14444159 1.832671954 0.000874015 MAP2K1sg1 + TUBA1Asg2 + FGF2sg1 −1.143281836 1.855410733 0.079298522 MTORsg2 + MTORsg1 + TYMSsg3 −1.142964931 1.368734858 0.284222949 IKBKBsg2 + TOP1sg1 + PIK3C3sg2 −1.14259162 2.722771563 0.007104798 ERBB2sg1 + IKBKBsg1 + TYMSsg3 −1.141496339 1.633260489 0.058688468 TOP1sg1 + TUBA1Asg2 + TGFB1sg

−1.141348167 1.558562976 0.25011195 PIK3C3sg

 + HDAC1sg1 + PIK3C3sg1 −1.140150144 1.501711587 0.222882396 CDK4sg3 + TUBA1Asg1 + TYMSsg

−1.138107172 1.627570659 0.234347004 DNMT1sg1 + ERBB2sg1 + IKBKBsg1 −1.137935223 1.726508036 0.210664536 TOP1sg2 + HDAC1sg

 + TYMSsg3 −1.137818

94 2.358672397 0.014198547 EGFRsg2 + TYMSsg3 + ERBB2sg2 −1.137373555 1.406459772 0.112237805 POLA1sg1 + TOP1sg2 + dummysg1 −1.136584813 1.373590084 0.074097921 FGF2sg1 + TUBA1Asg1 + MTORsg2 −1.135968062 1.845683741 0.171590957 POLA1sg1 + TUBA1Asg1 + PIK3C3sg1 −1.135284304 1.362681692 0.304612944 TYMSsg3 + IKBKBsg2 + DNMT1sg1 −1.134876433 1.799255 0.036245383 POLA1sg2 + PIK3C3sg2 + FGF2sg2 −1.133727846 1.423469134 0.069770485 POLA1sg1 + DNMT1sg1 + PIK3C3sg2 −1.133

36805 2.640238775 0.010551881 CDK4sg2 + PIK3C3sg1 + DNMT1sg2 −1.133559205 1.493413459 0.284482584 DNMT1sg1 + FGF2sg2 + MAP2K1sg1 −1.133140355 1.763010245 0.207353379 MTORsg2 + FGF2sg1 + MAP2K1sg2 −1.132776145 1.759426251 0.035838701 dummysg2 + FGF2sg2 + FGF2sg1 −1.132

74718 1.530021495 0.05585562 DNMT1sg2 + CDK4sg3 + FGF2sg1 −1.132532444 1.997515973 0.023001441 IKBKBsg1 + TOP1sg1 + TYMSsg3 −1.13236637 1.428914169 0.218435995 TOP1sg2 + dummysg2 + IKBKBsg2 −1.132317866 1.787864874 0.200600814 FGF2sg1 + TOP1sg1 + MAP2K1sg1 −1.132360541 1.924580305 0.000798282 PIK3C3sg2 + POLA1sg2 + TYMSsg1 −1.131733068 1.301484044 0.069137493 TGFB1sg1 + TOP1sg2 + POLA1sg1 −1.130317543 2.350623873 0.059183679 IKBKBsg2 + EGFRsg1 + EGFRsg2 −1.127895057 2.480054306 0.00361

356 HDAC1sg1 + MTORsg2 + PIK3C3sg2 −1.127482332 1.580557419 0.20

915228 dummysg2 + IKBKBsg2 + TYMSsg1 −1.12723029 1.481455998 0.015119952 CDK4sg2 + CDK4sg3 + MAP2K1sg1 −1.127225949 1.534167545 0.218369056 FGF2sg2 + FGF2sg2 + TYMSsg3 −1.127074535 2.203567161 0.005301891 MTORsg1 + DNMT1sg1 + DNMT1sg1 −1.126596345 2.821172645 0.00273687 IKBKBsg2 + TUBA1AsG2 + TYMSsg3 −1.126324104

.664157524 0.15743942 TGFB1sg2 + PIK3C3sg2 + PIK3C3sg2 −1.126160139 1.550012439 0.208351352 PIK3C3sg2 + PIK3C3sg2 + DNMT1sg1 −1.126099866 1.856373285 0.034342235 dummysg2 + POLA1sg1 + FGF2sg1 −1.125899684 1.895786185 0.030613928 POLA1sg1 + FGF2sg1 + TGFB1sg1 −1.125015815 3.253557332 0.004500352 EGFRsg2 + POLA1sg2 + ERBB2sg

−1.124499689 2.69803359 0.003906682 FGF2sg2 + IKBKBsg2 + TGFB1sg2 −1.123397461 1.34502795 0.01959

908 MAP2K1sg1 + TUBA1Asg2 + EGFRsg2 −1.123279112 1.358786502 0.054173476 TYMSsg3 + TYMSsg3 + HDAC1sg2 −1.122772617 1.344752159 0.26375

393 TGFB1sg1 + HDAC1sg

 + HDAC1sg1 −1.121228285 1.594580506 0.048558778 PIK3C3sg1 + TUBA1Asg1 + TGFB1sg2 −1.121057692 1.528023712 0.00188

0

1 TYMSsg3 + FGF2sg1 + MTORsg1 −1.120674045 2.067346039 0.14184078 TYMSsg3 + TOP1sg2 + HDAC1sg1 −1.119915476 2.182787264 0.069767841 FGF2sg1 + PIK3C3sg2 + TYMSsg3 −1.119550824 1.419186871 0.129823151 IKBKBsg2 + MTORsg2 + IKBKBsg2 −1.118315484 1.4

2488721 0.279363489 DNMT1sg1 + PIK3C3sg2 + TGFB1sg2 −1.116678201 1.421174315 0.175720955 dummysg2 + FGF2sg2 + IKBKBsg2 −1.116045852 1.508525989 0.061266813 DNMT1sg1 + TOP1sg2 + FGF2sg1 −1.113380593 2.053198004 0.020721063 MTORsg2 + ERBB2sg1 + dummysg1 −1.111472213 1.743074341 0.031017277 TOP1sg1 + ERBB2sg1 + MAP2K1sg1 −1.110997223 1.697095796 0.07530

004 CDK4sg3 + TOP1sg1 + PIK3C3sg2 −1.105967935 1.511399934 0.035839345 ERBB2sg1 + MTORsg1 + PIK3C3sg2 −1.105203606 2.02410231

0.017124158 TYMSsg3 + ERBB2sg2 + TGFB1sg

−1.104787772 1.493557721 0.056575806 CDK4sg3 + ERBB2sg2 + PIK3C3sg1 −1.104408717 1.446979283 0.059363987 PIK3C3sg2 + TYMSsg3 + POLA1sg1 −1.104312527 1.418563969 0.064415228 CDK4sg3 + dummysg1 + ERBB2sg1 −1.104144153 1.455259107 0.11043939 TGFB1sg1 + MTORsg2 + POLA1sg1 −1.103814502 1.635652436 0.096050578 FGF2sg2 + TOP1sg2 + CDK4sg2 −1.103615764 1.452870117 0.054108549 DNMT1sg2 + MAP2K1sg1 + ERBB2sg1 −1.101608379 1.858782877 0.093736183 EGFRsg1 + TYMSsg3 + TOP1sg2 −1.100988632 1.654099287 0.223477529 ERBB2sg2 + TYMSsg1 + EGFRsg2 −1.098943383 1.498888875 0.240995125 PIK3C3sg2 + DNMT1sg2 + EFGRsg2 −1.093789969 1.668808854 0.024665763 POLA1sg1 + MAP2K1sg2 + HDAC1sg2 −1.089949076 1.354809221 0.073746201 POLA1sg1 + POLA1sg1 + MAP2K1sg2 −1.089207806 1.861

263 0.10914

752 EGFRsg

 + CDK4sg2 + ERBB2sg1 −1.089041256 1.513316633 0.053420635 dummysg2 + TGFB1sg1 + TYMSsg3 −1.088712

58 1.609852188 0.030874416 dummysg1 + POLA1sg1 + TGFB1sg2 −1.088513703 1.364801587 0.221315474 TUBA1Asg1 + TYMSsg3 + PIK3C3sg1 −1.086317851 1.301572177 0.29438552 FGF2sg1 + TUBA1Asg2 + ERBB2sg2 −1.08582198 2.890735446 0.002669589 EGFRsg

 + TOP1sg1 + TUBA1Asg1 −1.085100042 1.394948614 0.300637565 TOP1sg1 + DNMT1sg1 + MAP2K1sg2 −1.084727485 1.342246917 0.302411679 IKBKBsg1 + TYMSsg3 + EGFRsg1 −1.084027293 1.34794809 0.242376346 MTORsg2 + DNMT1sg1 + dummysg2 −1.08073537 1.402367504 0.302015752 MTORsg2 + IKBKBsg2 + TYMSsg3 −1.079708996 2.26214343 0.107034979 dummysg2 + POLA1sg

 + TGFB1sg1 −1.078108479 2.060997561 0.004288599 HDAC1sg2 + IKBKBsg1 + FGF2sg2 −1.077197619 1.491979313 0.052455964 POLA1sg2 + DNMT1sg2 + FGF2sg2 −1.076641149 1.309803388 0.214087764 POLA1sg2 + HDAC1sg1 + EGFRsg2 −1.075070579 2.362517263 0.011571347 TGFB1sg2 + dummysg1 + TYMSsg3 −1.074945658 1.489987132 0.057044053 FGF2sg2 + PIK3C3sg1 + TGFB1sg2 −1.07433144 1.369438057 0.069446795 TYMSsg3 + TOP1sg1 + EGFRsg1 −1.073304382 1.476498913 0.058005522 TOP1sg1 + IKBKBsg1 + TYMSsg3 −1.069813006 1.399067002 0.066266294 TUBA1Asg1 + dummysg2 + HDAC1sg2 −1.067303256 1.555961947 0.048515633 TGFB1sg1 + TYMSsg3 + ERBB2sg1 −1.05620204 1.65373503 0.164256053 dummysg1 + CDK4sg3 + IKBKBsg2 −1.065481662 1.771998129 0.191430575 EGFRsg2 + MAP2K1sg1 + ERBB2sg1 −1.064279106 2.248873748 0.014196757 HDAC1sg2 + FGF2sg2 + MAP2K1sg1 −1.061970628 1.61387394 0.025658032 IKBKBsg

 + MTORsg2 + TGFB1sg2 −1.061922967 1.426042562 0.029966019 TUBA1Asg1 + IKBKBsg2 + MTORsg1 −1.061304443 1.309639435 0.073453688 POLA1sg2 + CDK4sg3 + DNMT1sg2 −1.060141021 2.255213848 0.107620503 PIK3C3sg2 + IKBKBsg1 + FGF2sg2 −1.05992252 1.578290707 0.044523215 POLA1sg1 + PIK3C3sg1 + DNMT1sg1 −1.056882265 1.665449097 0.189147542 HDAC1sg2 + TGFB1sg2 + TUBA1Asg1 −1.056699824 1.33128289 0.28679205 PIK3C3sg2 + TUBA1Asg2 + MAP2K1sg

−1.056330967 1.594031712 0.168044915 FGF2sg1 + CDK4sg3 + TUBA1Asg2 −1.054927078 1.972920236 0.018632744 MAP2K1sg1 + TYMSsg1 + TUBA1Asg2 −1.05479086 1.323675624 0.074839836 HDAC1sg1 + TOP1sg2 + HDAC1sg2 −1.054151618 1.35195666 0.184190344 MAP2K1sg2 + IKBKBsg1 + EGFRsg1 −1.053206974 1.550664753 0.211614969 IKBKBsg1 + TYMSsg1 + MAP2K1sg2 −1.051655076 2.505416923 0.058800479 TOP1sg2 + FGF2sg1 + TYMSsg3 −1.051291448 1.494232789 0.202822077 HDAC1sg1 + HDAC1sg2 + PIK3C3sg1 −1.050448251 1.869698788 0.108197732 TYMSsg3 + MAP2K1sg1 + DNMT1sg1 −1.050325041 1.844012231 0.028039119 PIK3C3sg2 + TYMSsg3 + PIK3C3sg

−1.04981959 1.60504699 0.16224253 MAP2K1sg2 + PIK3C3sg1 + TYMSsg3 −1.049017082 1.602268841 0.230554585 CDK4sg3 + TOP1sg2 + TYMSsg

−1.048797901 1.35279951 0.069827759 ERBB2sg1 + dummysg1 + DNMT1sg1 −1.048564422 1.805456928 0.031430367 IKBKBsg1 + TUBA1Asg1 + TOP1sg2 −1.046859265 1.387320534 0.038589388 ERBB2sg1 + MTORsg1 + ERBB2sg2 −1.04685217 1.659287788 0.037983581 CDK4sg2 + TYMSsg1 + EGFRsg2 −1.046604154 1.434454332 0.206001389 TOP1sg2 + dummysg2 + PIK3C3sg1 −1.045727354 3.307624235 0.028178957 PIK3C3sg2 + FGF2sg2 + ERBB2sg1 −1.045521646 1.911586919 0.10125078 MAP2K1sg2 + PIK3C3sg2 + MAP2K1sg1 −1.044763318 2.760268469 0.053525561 IKBKBsg

 + MAP2K1sg2 + dummysg2 −1.043399039 1.491699965 0.046041363 MAP2K1sg1 + EGFRsg1 + TYMSsg1 −1.042770511 1.451152065 0.019766743 PIK3C3sg2 + dummysg1 + FGF2sg1 −1.042619078 1.612770077 0.027939033 EGFRsg2 + CDK4sg3 + TUBA1Asg1 −1.042095003 1.40539201 0.021749746 MAP2K1sg1 + POLA1sg1 + POLA1sg1 −1.042088946 1.409509498 0.09875165 ERBB2sg1 + MTORsg2 + HDAC1sg2 −1.039184463 1.545996653 0.24444033 MTORsg1 + TYMSsg3 + TUBA1Asg1 −1.036220029 1.469166839 0.187641509 MAP2K1sg2 + EGFRsg2 + dummysg1 −1.035891124 1.827881391 0.150119759 MTORsg1 + TUBA1Asg2 + FGF2sg1 −1.031131295 1.358441718 0.169591371 MAP2K1sg1 + IKBKBsg2 + DNMT1sg1 −1.028480128 2.452492383 0.075899532 PIK3C3sg2 + EGFRsg1 + PIK3C3sg2 −1.028396161 1.703512809 0.028102288 dummysg1 + POLA1sg2 + TGFB1sg2 −1.028247249 1.350151145 0.069865046 TYMSsg1 + TOP1sg1 + CDK4sg2 −1.02786201 1.523391298 0.045331376 dummysg2 + dummysg2 + MTORsg2 −1.027528536 1.549150015 0.031423552 ERBB2sg1 + MAP2K1sg2 + TOP1sg2 −1.027031671 1.315004453 0.07169944 ERBB2sg1 + EGFRsg1 + MAP2K1sg2 −1.026577745 1.403239392 0.031834491 FGF2sg2 + MAP2K1sg2 + TYMSsg3 −1.025284194 1.593692775 0.045765419 HDAC1sg2 + PIK3C3sg2 + PIK3C3sg1 −1.025200053 2.327372667 0.014714297 POLA1sg1 + TUBA1Asg1 + dummysg1 −1.02515291 1.6

468873 0.140280168 HDAC1sg1 + PIK3C3sg2 + TYMSsg1 −1.02367703 1.407843558 0.061485372 ERBB2sg1 + TOP1sg2 + FGF2sg1 −1.02340871 2.048694692 0.049579866 FGF2sg1 + PIK3C3sg2 + MTORsg1 −1.023374667 1.480813966 0.244072838 TGFB1sg2 + FGF2sg2 + HDAC1sg1 −1.022838504 1.995524606 0.014766344 MTORsg1 + TYMSsg1 + TUBA1Asg1 −1.02212387 1.481796217 0.1014738 dummysg1 + TOP1sg1 + TYMSsg3 −1.021882262 1.805184677 0.032450708 MTORsg2 + ERBB2sg1 + DNMT1sg1 −1.020431238 1.770303053 0.126084679 HDAC1sg1 + TOP1sg2 + EGFRsg1 −1.018970675 2.238361309 0.014085636 HDAC1sg1 + TUBA1Asg3 + MAP2K1sg1 −1.018863795 1.532971936 0.049640575 TYMSsg3 + DNMT1sg2 + TOP1sg1 −1.018599742 1.847948284 0.161970178 TYMSsg3 + FGF2sg1 + PIK3C3sg2 −1.018270761 1.848550837 0.114524997 IKBKBsg1 + TOP1sg2 + ERBB2sg1 −1.018081131 1.350091747 0.2824869 TGFB1sg1 + TYMSsg3 + PIK3C3sg2 −1.017220322 2.237929101 0.059632539 EGFRsg1 + EGFRsg1 + TUBA1Asg1 −1.014847535 1.380807902 0.061106548 CDK4sg3 + TOP1sg

 + EGFRsg2 −1.013832049 1.565015023 0.043914797 PIK3C3sg2 + DNMT1sg1 + POLA1sg1 −1.013699482 1.51390063 0.242394832 HDAC1sg1 + FGF2sg2 + TUBA1Asg1 −1.013599278 1.367585581 0.095516221 CDK4sg2 + DNMT1sg2 + IKBKBsg2 −1.013469726 1.398370027 0.058733254 POLA1sg1 + TYMSsg3 + MTORsg1 −1.013081108 1.574371786 0.016648136 IKBKBsg1 + TOP1sg1 + DNMT1sg1 −1.012172158 1.493071444 0.052098454 DNMT1sg2 + MAP2K1sg1 + PIK3C3sg2 −1.011583822 1.434992297 0.040954863 MAP2K1sg1 + DNMT1sg1 + TYMSsg3 −1.0115148 2.280910825 0.008280712 TOP1sg2 + FGF2sg2 + FGF2sg2 −1.011490201 1.46570

677 0.055615704 PIK3C3sg2 + DNMT1sg1 + TYMSsg3 −1.010822086 1.405918167 0.058254872 IKBKBsg2 + MTORsg2 + dummysg1 −1.008795131 1.335661661 0.068797135 EGFRsg1 + TUBA1Asg1 + TOP1sg2 −1.008098858 1.515588025 0.051195701 TYMSsg3 + TOP1sg2 + DNMT1sg2 −1.007584193 2.092769785 0.102106864 DNMT1sg2 + TUBA1Asg2 + FGF2sg

−1.004581173 1.352614099 0.257999131 CDK4sg2 + EGFRsg2 + dummysg2 −1.004067447 1.645074165 0.033489346 IKBKBsg2 + PIK3C3sg2 + PIK3C3sg2 −1.000882226 1.457871575 0.086327258 ERBB2sg1 + EGFRsg2 + TUBA1Asg1 −1.000425196 1.320948904 0.071216397

indicates data missing or illegible when filed

TABLE S7 List of paired gene-targeting gRNA combinations identified with a mean log2 ratios of <−1 in the ovarian cancer study gRNA Mean CV combination log₂ FC −log₁₀ P (SD/mean FC) ATP1A1sg2 + HDAC1sg1 −6.054613745 1.881119566 0.170362768 TYMSsg1 + ATP1A1sg1 −2.885498992 1.112433655 0.116175689 NR3C1sg3 + PARP1sg1 −2.360449186 1.030396194 0.129592963 ACAA1sg2 + METAP2sg1 −2.236962359 1.21985688 0.714141117 TOP1sg1 + DHODHsg3 −2.213594239 1.076688357 0.685629225 COMTsg2 + APEX1sg1 −2.197610948 1.382488015 0.417587195 TUBA1Asg2 + POLA1sg3 −2.086345716 1.14499346 0.139632171 FGF2sg2 + POLA1sg3 −1.946446079 1.192383699 0.319906915 CDK2sg3 + TUBA1Asg1 −1.855937521 1.222990736 0.066128628 AKT1sg2 + NPC1L1sg3 −1.834221126 1.826734428 0.307167104 ATP1A1sg1 + FASNsg3 −1.831916258 1.67740076 0.071458503 METAP2sg3 + SLC12A4sg3 −1.816260337 1.304115744 0.059697437 COMTsg3 + NR3C1sg3 −1.709675992 1.093138968 0.117018746 AKT1sg3 + NR3C1sg3 −1.593906482 1.178066558 0.428367775 POLA1sg3 + CYP5

A1sg3 −1.575347213 1.016781774 0.583237296 CPT2sg3 + SOAT1sg1 −1.551144138 1.41007839 0.087276054 CDK2sg3 + PDGFRBsg3 −1.539592897 1.280364856 0.073588161 RRM1sg1 + K

AP1sg1 −1.53364194 1.088395165 0.299773034 METAP2sg3 + IMPDH2sg1 −1.483445771 1.404411204 0.029014313 CPT2sg2 + DHODHsg3 −1.481470367 1.623918197 0.062509253 RRM1sg2 + AKT1sg2 −1.474248353 1.064390667 0.244332361 KDM4Csg2 + MAP2K1sg3 −1.462083813 1.363102834 0.044744207 DNMT1sg2 + PARP1sg2 −1.461604733 1.249766696 0.182284636 TOP1sg1 + TGFB1sg2 −1.4437489 1.13865193 0.110550361 MTORsg2 +

GFR1sg1 −1.423678518 1.008760747 0.61151819 ATP1A1sg3 + VKORC1sg1 −1.40146029 1.042528941 0.089147215 RRM1sg1 + DHODHsg1 −1.385167044 1.263285904 0.109798244 ERBB2sg1 + TUBA1Asg2 −1.375136762 3.230879874 0.032090282 TUBA1Asg3 + CPT2sg1 −1.373305753 1.611400931 0.042623957 FKBP1Asg1 + CDK2sg1 −1.369824741 1.811887735 0.199048832 CYP51A1sg3 + PSMB1sg2 −1.342444384 2.187253967 0.144647752 MAPK3sg1 + ERBB2sg2 −1.325842165 1.052165909 0.255670566 VKORC1sg2 + GSRsg3 −1.324384925 1.139659189 0.136392037 RRM1sg2 + CDK2sg3 −1.319583016 1.356718188 0.043625996 SLC12A4sg2 + PSMB1sg1 −1.315487135 1.212373434 0.140946871 TOP1sg3 + NPC1L1sg1 −1.30297574 1.183486305 0.467263738 FKBP1Asg1 + ABCC1sg1 −1.288582058 1.105190675 0.500642482 TYMSsg1 + ALDH2sg3 −1.283238562 1.195052482 0.078223835 ATP1A1sg3 + HDAC1sg2 −1.275831548 1.032925567 0.194950393 PRDX5sg3 + NPC1L1sg3 −1.259840994 1.049431152 0.175093796 MTORsg1 + KEAP1sg1 −1.241315287 1.103636413 0.135036233 TUBA1Asg2 + CDK2sg3 −1.236336082 1.303817233 0.080944685 RRM1sg2 + VKORC1sg1 −1.232905758 1.086286846 0.406853521 ERBB2sg3 + NPC1L1sg3 −1.226697529 1.041558819 0.114251423 RRM1sg2 + TYMSsg2 −1.202729599 1.397302294 0.07612401 DHODHsg2 + CYP51A1sg1 −1.200851128 1.503866643 0.257472934 TUBA1Asg2 + DHODHsg2 −1.199131703 1.011850391 0.147283926 GANABsg3 + CDK2sg1 −1.19910792 1.576574523 0.01750731 MTORsg2 + ERBB2sg2 −1.192252627 2.177211296 0.002233725 PIK3C3sg1 + NPC1L1sg1 −1.178868313 1.041055129 0.163816652 IMPDH2sg1 + CDK4sg1 −1.173072095 1.157532042 0.368018709 PDGFRBsg2 + ERBB2sg3 −1.172199543 1.133511239 0.154661116 PDGFRBsg1 + SLC12A4sg3 −1.150437491 1.418002013 0.049822087 TYMSsg3 + CDK4sg1 −1.149918859 1.49595429 0.015648445 FDPSsg1 + ACAA1sg3 −1.14019043 1.041161078 0.061584103 HPRT1sg1 + APEX1sg2 −1.135621963 1.054710364 0.101757948 TGFB1sg1 + MTORsg2 −1.1305757 1.401360149 0.044185824 CDK2sg2 + METAP2sg3 −1.123373652 1.05709745 0.474288019 FGF2sg2 + ERBB2sg1 −1.119450004 1.26663269 0.002632273 TYMSsg1 + KEAP1sg3 −1.111937992 1.278688299 0.077348664 GSRsg2 + KDM6Bsg1 −1.111483307 1.100280088 0.41966873 FGFR1sg3 + FGF2sg2 −1.101357364 1.150600563 0.145497129 FKBP1Asg2 + CDK2sg3 −1.092645496 1.893692554 0.169494671 RRM1sg1 + SLC12A4sg3 −1.092425079 1.47255856 0.264933789 ERBB2sg1 + PARP1sg2 −1.080562448 1.017373632 0.480876984 MTORsg1 + FASNsg1 −1.079373731 1.538747894 0.045631505 M6PRsg3 + METAP2sg2 −1.067076981 1.08270709 0.389287665 M6PRsg1 + KDM6Bsg1 −1.054733858 1.21695119 0.053956326 PARP1sg2 + DNMT1sg3 −1.052586175 1.52508478 0.024731919 TUBA1Asg1 + NPC1L1sg2 −1.036064931 1.108181342 0.055155122 EGFRsg1 + TGFB1sg2 −1.035102587 1.246334093 0.34801711 METAP2sg3 + CDK4sg3 −1.031224671 1.405802324 0.057179297 DHODHsg1 + APEX1sg3 −1.018299592 1.064623952 0.343032484 FGFR1sg3 + SLC25A5sg2 −1.009431625 1.216933819 0.165241198 SOAT1sg1 + PIK3C3sg1 −1.006515271 1.313912995 0.072098036 GSRsg3 + APEX1sg1 −1.00550777 1.031073841 0.118029864

indicates data missing or illegible when filed

Cell Viability Assay and Drug Interaction Analysis

1,500 OVCAR8-ADR cells were seeded onto one well of a 96-well plate one day prior to drug treatment. 4,800 SK-N-MC cells were seeded onto one well of a 96-well plate and were pre-treated with the drug(s) for 72 hours, followed by adding rotenone (Abcam, ab143145) or MPP⁺ (Abcam, ab144783) to induce toxicity. Drugs were applied at indicated doses. Azacitidine (A-5959), olaparib (0-9201), sirolimus (R-5000), seliciclib (R-1234), lapatinib (L-4899), erlotinib (E4007), and vorinostat (V-8477) were purchased from LC Laboratories. Fludarabine (#14128) was purchased from Cayman Chemical Company. 17-DMAG (A2213) was purchased from ApexBio. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay was performed, as described previously (Wong et al., 2015), to assess cell growth at different time points. Briefly, medium in the cell growing wells were replaced by 100 ul of 1×MTT solution in RPMI 1640 without phenol red and incubated at 37° C. with 5% CO₂ for 3 hrs. Then 100 μl solubilization buffer (10% Triton X-100, 0.1N HCl in isopropanol) are applied to each well to dissolve the blue formazan crystals. The absorbance was measured at 570 nm and 650 nm by VARIOSKAN FLASH microplate reader (Thermo Scientific). Bliss independent (Bliss, 1939) and HSA (Borisy et al., 2003) models were adopted for evaluating interactions between drug pairs, and DiaMOND model (Cokol et al., 2017; Cokol-Cakmak et al., 2018) was used for measuring three-way drug interactions. The excess over Bliss independent model was calculated as, g12−(g1+g2−g1×g2/100), where g indicates the percentage of growth inhibition, the number indicates the drug component; the excess over HSA model was calculated by subtracting the highest growth inhibition effect of single agent from that of the combination; the DiaMOND model was used for calculating the frictional inhibitory concentration (FIC₃), which equals (o1+o2+o3)/((e1+e2+e3)/3), where o indicates the observed concentration of each component in the combination, and e indicates the expected concentration of individual drugs at certain inhibitory level, which is determined by drug response curves. To generate the drug response curves, the three drugs were combined in a fixed ratio of 1:1:1 of their respective IC₅₀ and scaled proportionally. If FIC₃ is <1, the interaction is synergistic; if FIC₃ is =1, the interaction is additive; and if FIC₃ is >1, the interaction is antagonistic.

Colony Formation Assay

1,000 OVCAR8-ADR cells were seeded onto one well of a 6-well plate one day prior to drug treatment at indicated doses. Colonies were fixed by ice-cold methanol at −20° C. for 30 min and stained by crystal violet. Colony number and area were determined by ImageJ software.

Pseudopupil Assay

Wild-type and transgenic Drosophila strains carrying gmr-GAL4 and UAS-α-syn(Auluck et al., 2002) were used. gmr-GAL4 female flies were crossed with w¹¹¹⁸ (control) or UAS-α-syn male flies, and raised at 21.5° C. on cornmeal medium supplemented with drug(s) or vehicle control. Drug treatment was performed by adding vorinostat (LC Laboratories, V-8477) and/or 17-DMAG (InvivoGen, ant-dgl-25) into 2 ml of the medium at final concentrations of 0.5 μM and 96 μg/ml, respectively. After eclosion, progeny were transferred into a new vial with medium supplemented with fresh drug(s), and the drug(s) were changed every 3-4 days prior to the assay. Eyes of 7- to 11-day-old flies were examined under a light microscope (Olympus CX31) with a 60× oil objective as described previously (Wong et al., 2008). At least 100 ommatidia from 5-10 flies were examined and the number of rhabdomeres were recorded.

RNA-Seq

Total RNAs were isolated from drug-treated OVCAR8-ADR cells by MiniBEST universal RNA extraction kit (Takara). RNA samples were quantified and analysed using Qubit assay and high-sensitivity DNA chip (Agilent) on an Agilent 2100 Bioanalyzer, respectively. RNA-seq experiments were performed at the Centre for Genomic Sciences (LKS Faculty of Medicine, The University of Hong Kong). The Illumina adaptors of the paired-end raw sequence reads were trimmed by Trimmomatic 0.39. The STAR aligner version 2.7 was used to align the sequence reads to the human genome, where the genome index was built using the primary assembly of Gencode's version 30 release of the human genome. The raw count reads were extracted using the R package Rsubread. R packages EdgeR, limma, and HTSFilter were used for differential expression analysis comparing each of the pairwise and three-way drug combinations with the untreated samples. An FDR<0.05 filter was applied for the three-way combination versus untreated samples while an FDR<1 filter was applied for each of the two-way combinations versus untreated samples. The combinations and the genes were clustered by complete-linkage clustering, where the distance is defined as 1-Pearson correlation. The genes that were at least 20% up- or down-regulated in cells treated with the three-drug regimen when compared to the untreated control were inputted into DAVID web tools for pathway analysis, and the Reactome pathway database was used. The pathway mapping used a P=0.05 threshold.

Quantification and Statistical Analysis

Data analyses were performed using GraphPad Prism 7 software (GraphPad Software). Data expressed are mean±SD, biological replicates are specified for each experiment in figure legends. Statistical comparisons between two groups were carried out by Student t-test, whereas one-way ANOVA followed by Tukey's or Dunnett's post hoc tests were used for comparisons of groups more than two.

Data and Code Availability

All sequencing data generated or analysed during this study are available.

Key Resources Table

REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Zeocin Life Technologies Cat#R25001 FuGene HD transfection reagent Promega Cat#E2312 Polybrene Sigma Cat#TR-1003-G Propidium iodide Invitrogen Cat#BMS500PI Rotenone Abcam Cat#ab143145 MPP⁺ Abcam Cat#ab144783 Azacitidine LC Laboratories Cat#A-5959 Olaparib LC Laboratories Cat#O-9201 Sirolimus LC Laboratories Cat#R-5000 Seliciclib LC Laboratories Cat#R-1234 Lapatinib LC Laboratories Cat#L-4899 Erlotinib LC Laboratories Cat#E4007 Vorinostat LC Laboratories Cat#V-8477 Fludarabine Cayman Chemical Cat#14128 Company 17-DMAG InvivoGen Cat#ant-dgl-25 Critical Commercial Assays Quant-iT PicoGreen dsDNA Assay kit Life Technologies Cat#P11496 Kapa HiFi Hotstart Ready-mix Kapa Biosystems Cat#KK2602 Agencourt AMPure XP beads Beckman Coulter Cat#A63881 Genomics Kapa SYBR Fast qPCR Master Mix Kapa Biosystems Cat#KK4600 Experimental Models: Cell Lines HEK293T (female) ATCC CRL-3216 SK-N-MC (female) ATCC HTB-10 OVCAR8-ADR (female) Honma et al., 2008 N/A KURAMOCHI (female) JCRB JCRB0098 OVSAHO (female) JCRB JCRB1046 Experimental Models: Organisms/Strains GMR-GAL4 (Drosophila strain) FlyBase FBtp0018010 UAS-α-synuclein (Drosophila strain) FlyBase FBtp0012468 Oligonucleotides All gRNAs used are listed in Table S3 This paper N/A Recombinant DNA All plasmid constructs are listed in Table S5 This paper N/A Software and Algorithms inDelphi Shen et al., 2018 http://indelphi.giffordlab.mit.edu/ FORECasT Allen et al., 2019 https://github.com/felicityallen/SelfTarget FlowJo v10.5.3 Becton Dickinson N/A R package DescTools Signorell et al., 2019 https://CRAN.R-project.org/package=DescTools ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ R package Rsubread Liao et al., 2019 10.18129/B9.bioc.Rsubread R packages EdgeR Robinson et al, 2010 10.18129/B9.bioc.edgeR limma Ritchie et al., 2015 10.18129/B9.bioc.limma HTSFilter Rau et al., 2013 10.18129/B9.bioc.HTSFilter DAVID web tools Huang et al., 2009 https://david.ncifcrf.gov/ Reactome pathway database Fabregat et al., 2018 https://reactome.org/ GraphPad Prism 7 GraphPad Software N/A

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The foregoing description of the specific embodiments will so fully reveal the general nature of the disclosure that others can, by applying knowledge within the skill of the relevant art(s) (including the contents of the documents cited and incorporated by reference herein), readily modify and/or adapt for various applications such specific embodiments, without undue experimentation, without departing from the general concept of the present disclosure. Such adaptations and modifications are therefore intended to be within the meaning and range of equivalents of the disclosed embodiments, based on the teaching and guidance presented herein. It is to be understood that the phraseology or terminology herein is for the purpose of description and not of limitation, such that the terminology or phraseology of the present specification is to be interpreted by the skilled artisan in light of the teachings and guidance presented herein, in combination with the knowledge of one skilled in the relevant art(s).

While various embodiments of the present disclosure have been described above, it should be understood that they have been presented by way of examples, and not limitation. It would be apparent to one skilled in the relevant art(s) that various changes in form and detail could be made therein without departing from the spirit and scope of the disclosure. Thus, the present disclosure should not be limited by any of the above-described exemplary embodiments but should be defined only in accordance with the following claims and their equivalents.

All references cited herein are incorporated herein by reference in their entirety and for all purposes to the same extent as if each individual publication or patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety for all purposes. 

1. A system for multiplexed genome editing or a two or three-way combinatorial CRISPR screening comprising: a lentiviral vector comprising human U6 (hU6) promoter, mouse U6 (mU6) promoter and human H1 (hH1) promoter expressing an array of three or more barcoded guide RNAs (“gRNAs”) oligo pairs, the promoters having a 3′ end comprising modified hU6, mU6 and hH1 promoter sequences for paired annealing of the barcoded gRNAs oligo pairs.
 2. A system for multiplexed genome editing or a two or three-way combinatorial CRISPR screening comprising: a lentiviral vector comprising human U6 (hU6) promoter, mouse U6 (mU6) promoter and human H1 (hH1) promoter expressing an array of three or more barcoded guide RNAs (“gRNAs”) oligo pairs, the hU6 promoter having an unmodified promoter sequence at 3′ end and the mU6 and hH1 promoters having modified promoter sequences at 3′ end for paired annealing of the barcoded gRNAs oligo pairs.
 3. The system of claim 1 wherein the paired annealing of the barcoded gRNAs oligo pairs form RNA scaffolds.
 4. The system of claim 1 wherein a combinatorial gRNA library is assembled by CombiGEM-CRISPR v2.0.
 5. The system of claim 1 wherein the lentiviral vector transfects human cells and the barcoded gRNAs are delivered to the human cells.
 6. The system of claim 1 further comprising quantitation of barcoded gRNAs using next-generation sequencing at a time point post transfection.
 7. The system of claim 1 wherein the three-way combinatorial CRISPR screen is a high-throughput screen.
 8. The system of claim 4 wherein the gRNAs form a RNA scaffold sequence comprising the same 3′ end of the modified hU6, mU6 and hi-1l promoter sequences as the combinatorial gRNA libraries.
 9. The system of claim 4 wherein the gRNAs form a RNA scaffold sequence comprising the same 3′ end of the hU6, mU6 and hH1 promoter sequences as the combinatorial gRNA libraries.
 10. A method to screen for at least a three-way drug target combination; said method comprises: (i) providing a gRNA library targeting druggable genes of HGSOC wherein each gene comprises an array of 3 gRNAs; (ii) transfecting human cells; and (iii) quantifying barcoded gRNAs using next-generation sequencing.
 11. A system to screen for at least a three-way drug target combination comprising: (i) providing a lentiviral three-way combinatorial gRNA expressing construct that express gRNAs; (ii) transfecting human cells with fluorescence reporter gene; and (iii) measuring percentage of cell population positive for fluorescence at a time period post-transfection.
 12. The system of claim 11 wherein the fluorescence is measured using a flow cytometry and wherein the fluorescence is GFP, RFP and BFP fluorescence.
 13. The system of claim 11 wherein the gRNAs target an exonic regions of green (GFP), red (RFP), and blue (BFP) fluorescent protein reporter genes.
 14. The system of claim 11 wherein the human cells are ovarian cancer cells.
 15. The system of claim 14 wherein the ovarian cancer cells are high-grade serous ovarian cancer (“HGSOC”) cells.
 16. The system of claim 15 wherein the ovarian cancer cells are OVCAR8-ADR and OVCAR8-ADR-Cas9.
 17. A method to screen for at least a three-way drug target combination comprising the steps of: (i) providing a lentiviral three-way combinatorial gRNA expressing construct that express gRNAs; (ii) transfecting human cells with fluorescence reporter gene; and (iii) measuring percentage of cell population positive for fluorescence at a time period post-transfection.
 18. The method of claim 17 further comprising validation of the three-way drug target combination by matching a drug to the drug target.
 19. The method of claim 17 wherein the three-way drug target combinations provides a three-drug regimen for a disease.
 20. The method of claim 17 wherein the fluorescence is GFP, RFP or BFP.
 21. The method of claim 17 wherein the at least a three-way drug target combination are synergistic combinations.
 22. The method of claim 19 wherein the disease is cancer or Parkinson's disease.
 23. A method to treat HGSOC comprising administering drugs that targets PARP1, DNMT1, CDK2, FKBP1A or a combination thereof.
 24. The method of claim 23 wherein the drug comprises Olaparib (OLA), azacitdine (AZA), seliciclib (SEL), sirolimus (SIR), or a combination thereof.
 25. The method of claim 24 wherein the drug comprises OLA and AZA.
 26. A system for CRISPR-based multi-gene knockout screening comprising a barcoded gRNA expression cassette comprising: (i) a first promoter operatively linked to a first gRNA; (ii) a second promoter operatively linked to a second gRNA; (iii) a third promoter operatively linked to a third gRNA; and (iv) three barcoded gRNA sequencing region, wherein the gRNA expression cassette is in a single vector.
 27. The system of claim 26 wherein the promoters are human U6, mouse U6, and Human H1 promoters and the three barcoded gRNA are modified gRNA scaffold variants.
 28. The system of claim 26 wherein the promoters comprises a modified 3′ end sequence which are complementary to the modified gRNA scaffold variants, said 3′ end sequence anneals to the modified gRNA scaffold variants.
 29. The system of claim 26 further comprising: (i) pooled digestion and ligation of the annealed 3′ end sequence and the gRNA scaffold variants to form an assembly of pooled barcoded combinatorial gRNA library.
 30. The system of claim 26 wherein the expression cassettes knockout target GFP gene in OVACR8-ADR-Cas9 cells.
 31. The system of claim 26 wherein the gRNA scaffold variants comprises: (i) higher on-target activity than wild-type scaffold; (ii) low off-target activities; and (iii) high on-to-off target activity.
 32. A system for CRISPR-based multi-gene knockout screening comprising a barcoded gRNA expression cassette comprising v3.11, v.3.12 or v.3.13. 